Tz-coli rMAP Comprehensive Analysis Report Summary

This run was generated using rMAP version performed on 2021-09-06… Thank you for using this pipeline!!

Quick links

• Assembly summary statistics

• SNP-Variant Calling

• Phylogenetic inference

• Antimicrobial Resistance Profiling

• Plasmid Profiling

• Virulence Factor Determination

• Multi-Locus Sequence Typing (MLST)

• Pangenome Analysis

• Insertion sequence characterization (IS)

• Citations and Bibliography

Assembly summary statistics

Field	Description
SampleID	Name of the sample
TrimReads	Total number of reads after quality filtering
MeanReadLen	Average read length after quality filtering
Contigs	Number of contigs of the draft genome (>200bp)
GenomeLength	Length (bp) of the draft genome
LargestContig	Length (bp) of the largest contig in the genome
N50	Length of the smallest contig in the set that contains the fewest (largest) contigs whose combined length represents at least 50% of the assembly
GC-Content	GC content (%) of the draft genome
Depth	Number of times each nucleotide position in the draft genome has a read that aligns to that position

SampleID	TrimReads	MeanReadLen	Contigs	GenomeLength	LargestContig	N50	GC-Content	Depth
ID002	333369	133	172	5085287	312914	82705	55.75	8X
ID003	616477	131	76	4958142	511081	157229	50.61	16X
ID005	597741	128	164	5503138	253294	123351	50.41	13X
ID006	301512	133	161	4746822	208611	76507	50.87	8X
ID007I	327125	133	185	5249858	251703	109545	50.71	8X
ID011	418346	131	82	5277658	650706	190638	50.64	10X
ID013I	387163	132	118	5538122	533025	136363	50.55	9X
ID016I	309087	128	506	10042668	155559	38849	51.18	3X
ID017	611344	128	64	4783983	652146	192648	50.76	16X
ID018CT	383929	131	162	4680922	202930	68081	50.78	10X
ID019	443475	130	83	4528078	318059	134785	50.83	12X
ID01CT	418836	132	124	4959035	276554	104113	50.37	11X
ID021	485729	129	90	4748880	254404	138297	50.81	13X
ID027	442579	131	98	4920875	273263	125768	50.74	11X
ID031	509794	132	175	4745888	203247	67378	50.86	14X
ID034I	391983	128	87	4880038	456762	129721	50.65	10X
ID041	432401	132	100	5118190	452947	130446	50.52	11X
ID043I	350630	132	140	5031536	335497	89537	50.70	9X
ID044	518343	131	195	4763310	219806	53942	50.84	14X
ID046II	374627	132	2766	5673652	47436	2787	50.56	8X
ID049	315807	132	184	4923578	164120	64560	50.92	8X
ID051	466053	127	88	5271445	420909	190646	50.64	11X
ID054	384818	130	72	4748190	417424	168080	50.75	10X
ID057	443440	130	97	4872584	314381	167129	50.63	11X
ID066II	417035	130	2706	8536351	47520	5347	50.78	6X
ID067	380913	131	112	4496530	321712	92781	50.71	11X
ID068	407122	129	92	4686877	413265	114183	50.86	11X
ID073I	378517	130	117	4708865	234463	82744	50.72	10X
ID077	384112	130	74	4771238	353848	159025	50.71	10X
ID081I	549895	132	187	4973038	393472	107669	50.91	14X
ID086II	379756	132	86	5276370	604349	173686	50.66	9X
ID088	341590	131	111	4875888	361498	103294	50.67	9X
ID092	295355	129	3641	10642645	49162	5656	46.53	3X
ID094LLFII	424681	132	2454	6006903	51042	4609	50.92	9X
ID099	507317	133	67	4785865	652158	159018	50.77	14X
ID09CT	501222	131	66	4851737	658072	160243	50.71	13X
ID101	466611	132	75	4832987	468479	183743	50.74	12X
ID107II	318782	130	142	5410692	380994	163449	50.51	7X
ID124	586457	131	111	4770741	254387	104390	50.74	16X
ID127	515705	132	100	4756092	254984	132888	50.85	14X
ID128	357615	129	69	5262738	614760	277261	50.69	8X
ID129E	417087	130	62	5133150	554479	170577	50.32	10X
ID130	311179	131	49	4661680	736056	217984	50.60	8X
ID134	605461	131	3877	6139040	129872	1884	50.17	12X
ID136	471997	128	94	4922299	414138	166152	50.64	12X
ID141	4076	135	652	417557	2966	625	51.28	1X
ID142	16216	135	3018	2987861	8838	1063	55.69	0X
ID164	536535	130	134	5079031	265992	106189	50.52	13X
ID169	309969	130	122	5282654	344280	127935	50.64	7X
ID177	390757	130	118	5106350	404038	148325	50.50	9X
ID178	505502	129	100	5482498	530211	232451	50.52	11X
ID182	429169	128	123	4432807	160909	68935	50.89	12X
ID186	427743	129	83	4903962	387978	166965	50.72	11X
ID187	383310	129	143	4887867	311668	104237	50.75	10X
ID195	316092	128	66	4855824	658270	152225	50.71	8X
ID197	531257	130	111	4886884	292160	112653	50.67	14X
ID199	333846	127	77	4921348	511673	225144	50.88	8X
ID208	359371	131	872	9916991	200836	30570	53.06	4X
ID214	295853	130	145	5110671	241561	101626	50.69	7X
ID224	562880	130	111	4892318	254085	109368	50.63	14X
ID228	456066	132	120	5454384	733279	178763	50.58	11X
ID229	408233	132	67	5032487	652101	193349	50.46	10X
ID231	373540	131	83	4771143	315548	149908	50.74	10X
ID233	481348	133	965	5340226	82272	11243	55.91	11X
ID235	419761	133	104	5226093	384333	190454	50.55	10X
ID237	424348	133	66	4988991	453590	190762	50.66	11X
ID256	346160	131	100	5321518	571968	170320	50.62	8X
ID263	313278	128	113	4838179	254390	113836	50.82	8X
ID282	275009	130	2801	8126081	61437	4871	50.80	4X
ORTHO013EI	380640	133	366	4758537	92560	30700	56.00	10X
ORTHO055E	258537	130	742	5612561	75585	15362	56.67	5X
ORTHO082EI	368868	128	162	5399453	315952	137911	51.60	8X
ORTHO08HW	403620	132	81	5112145	433351	127758	50.50	10X

Select the parameter

Number of reads

Average number of reads per sample = 405411

Average read length

Average read length per sample = 131 bp

Number of contigs

Average number of contigs per sample = 437

Genome length

Average genome length per sample = 5242466 bp

Largest contig length

Average largest contig length per sample = 340237 bp

N50

Average N50 per sample = 116894 bp

GC content

Average GC content per sample = 51.046%

Sequencing depth

Average sequencing depth = 9.822X

Back to index

SNP-variant calling

Field	Description
GenomePosition	Position in the genome where SNP is found
Type	Nature of the SNP identified (Only ‘True’ SNPs are shown by default)
ReferenceAllele	Allele found in the reference genome
AlternateAllele	Allele found in the genome of interest forming the SNP
Consequence	Amino acid alterations caused by the SNP
AffectedGene	The tartget gene affected by the SNP
Product	The outcome from the presence of the SNP

Select the sample

ID002

## Error in read.table("ID002_amr_snps", header = T, sep = "\t", dec = ".", : no lines available in input

## Error in as.data.frame(snps): object 'snps' not found

## Error in cbind(snps[, 1:7]): object 'snps' not found

## Error in colnames(snpsdata) = c("GenomePosition", "Type", "ReferenceAllele", : object 'snpsdata' not found

## Error in eval(expr, envir, enclos): object 'snpsdata' not found

## Error in row.names(snps) = NULL: object 'snps' not found

## Error in nrow(snps): object 'snps' not found

ID003

GenomePosition	Type	ReferenceAllele	AlternateAllele	Consequence	AffectedGene	Product
5732	snp	T	G	missense_variant c.728A>C p.Asp243Ala	yaaA	peroxide stress resistance protein YaaA
6239	snp	G	T	missense_variant c.221C>A p.Ala74Glu	yaaA	peroxide stress resistance protein YaaA
318076	snp	T	A	missense_variant c.244A>T p.Thr82Ser	rclC	reactive chlorine species resistance protein C
743181	snp	A	T	missense_variant c.355A>T p.Thr119Ser	ybgI	radiation resistance protein YbgI
1007522	snp	C	T	missense_variant c.79G>A p.Val27Ile	ycbX	6-N-hydroxylaminopurine resistance protein
1007576	snp	T	C	missense_variant c.25A>G p.Ile9Val	ycbX	6-N-hydroxylaminopurine resistance protein
1007587	snp	A	G	missense_variant c.14T>C p.Ile5Thr	ycbX	6-N-hydroxylaminopurine resistance protein
1216417	snp	G	T	missense_variant c.49G>T p.Ala17Ser	ariR	regulator of acid resistance, influenced by indole
1441506	snp	C	T	missense_variant c.238G>A p.Glu80Lys	hslJ	lipoprotein implicated in Novobiocin resistance
1500753	snp	G	A	missense_variant c.181G>A p.Ala61Thr	tehA	tellurite resistance protein
1620002	snp	C	T	missense_variant c.14C>T p.Ser5Leu	marB	multiple antibiotic resistance protein
1620022	snp	C	T	missense_variant c.34C>T p.Leu12Phe	marB	multiple antibiotic resistance protein
1620037	snp	G	A	missense_variant c.49G>A p.Ala17Thr	marB	multiple antibiotic resistance protein
1620046	snp	G	A	missense_variant c.58G>A p.Val20Ile	marB	multiple antibiotic resistance protein
1620120	snp	C	A	missense_variant c.132C>A p.His44Gln	marB	multiple antibiotic resistance protein
2227326	snp	G	A	missense_variant c.1433C>T p.Ala478Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227335	snp	C	A	missense_variant c.1424G>T p.Gly475Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227368	snp	G	A	missense_variant c.1391C>T p.Pro464Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227422	snp	G	C	missense_variant c.1337C>G p.Pro446Arg	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227443	snp	G	C	missense_variant c.1316C>G p.Ala439Gly	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227452	snp	A	C	missense_variant c.1307T>G p.Leu436Arg	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227563	snp	G	A	missense_variant c.1196C>T p.Pro399Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227653	snp	A	G	missense_variant c.1106T>C p.Ile369Thr	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227668	snp	A	G	missense_variant c.1091T>C p.Val364Ala	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227818	snp	G	A	missense_variant c.941C>T p.Pro314Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227935	snp	T	A	missense_variant c.824A>T p.Asn275Ile	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227949	snp	A	C	missense_variant c.810T>G p.Ser270Arg	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228109	snp	C	G	missense_variant c.650G>C p.Arg217Pro	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228145	snp	C	T	missense_variant c.614G>A p.Cys205Tyr	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228151	snp	C	A	missense_variant c.608G>T p.Arg203Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228190	snp	G	A	missense_variant c.569C>T p.Ala190Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228265	snp	G	A	missense_variant c.494C>T p.Pro165Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228349	snp	G	A	missense_variant c.410C>T p.Ala137Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228397	snp	G	C	missense_variant c.362C>G p.Ala121Gly	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228433	snp	C	A	missense_variant c.326G>T p.Arg109Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228444	snp	T	G	missense_variant c.315A>C p.Arg105Ser	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228502	snp	C	T	missense_variant c.257G>A p.Ser86Asn	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228553	snp	G	T	missense_variant c.206C>A p.Pro69His	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2630356	snp	G	A	missense_variant c.31G>A p.Ala11Thr	yfgI	nalidixic acid resistance protein YfgI
2630599	snp	T	A	missense_variant c.274T>A p.Ser92Thr	yfgI	nalidixic acid resistance protein YfgI
3635277	snp	C	T	missense_variant c.437C>T p.Thr146Ile	yhiM	inner membrane protein with a role in acid resistance
3635534	snp	T	A	missense_variant c.694T>A p.Phe232Ile	yhiM	inner membrane protein with a role in acid resistance
3869635	snp	C	T	missense_variant c.259C>T p.Leu87Phe	cbrA	colicin M resistance protein
3869965	snp	T	G	missense_variant c.589T>G p.Ser197Ala	cbrA	colicin M resistance protein
3869974	snp	A	G	missense_variant c.598A>G p.Asn200Asp	cbrA	colicin M resistance protein
3870080	snp	G	A	missense_variant c.704G>A p.Ser235Asn	cbrA	colicin M resistance protein
3870253	snp	A	G	missense_variant c.877A>G p.Thr293Ala	cbrA	colicin M resistance protein
3870258	snp	C	G	missense_variant c.882C>G p.Asp294Glu	cbrA	colicin M resistance protein
4103121	snp	G	T	missense_variant c.300G>T p.Met100Ile	yiiM	2-amino-6-N-hydroxylaminopurine resistance protein

ID005

GenomePosition	Type	ReferenceAllele	AlternateAllele	Consequence	AffectedGene	Product
5732	snp	T	G	missense_variant c.728A>C p.Asp243Ala	yaaA	peroxide stress resistance protein YaaA
6239	snp	G	T	missense_variant c.221C>A p.Ala74Glu	yaaA	peroxide stress resistance protein YaaA
318076	snp	T	A	missense_variant c.244A>T p.Thr82Ser	rclC	reactive chlorine species resistance protein C
743181	snp	A	T	missense_variant c.355A>T p.Thr119Ser	ybgI	radiation resistance protein YbgI
1007522	snp	C	T	missense_variant c.79G>A p.Val27Ile	ycbX	6-N-hydroxylaminopurine resistance protein
1007576	snp	T	C	missense_variant c.25A>G p.Ile9Val	ycbX	6-N-hydroxylaminopurine resistance protein
1007587	snp	A	G	missense_variant c.14T>C p.Ile5Thr	ycbX	6-N-hydroxylaminopurine resistance protein
1216417	snp	G	T	missense_variant c.49G>T p.Ala17Ser	ariR	regulator of acid resistance, influenced by indole
1441506	snp	C	T	missense_variant c.238G>A p.Glu80Lys	hslJ	lipoprotein implicated in Novobiocin resistance
1500753	snp	G	A	missense_variant c.181G>A p.Ala61Thr	tehA	tellurite resistance protein
1620002	snp	C	T	missense_variant c.14C>T p.Ser5Leu	marB	multiple antibiotic resistance protein
1620022	snp	C	T	missense_variant c.34C>T p.Leu12Phe	marB	multiple antibiotic resistance protein
1620037	snp	G	A	missense_variant c.49G>A p.Ala17Thr	marB	multiple antibiotic resistance protein
1620046	snp	G	A	missense_variant c.58G>A p.Val20Ile	marB	multiple antibiotic resistance protein
1620120	snp	C	A	missense_variant c.132C>A p.His44Gln	marB	multiple antibiotic resistance protein
2227326	snp	G	A	missense_variant c.1433C>T p.Ala478Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227335	snp	C	A	missense_variant c.1424G>T p.Gly475Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227368	snp	G	A	missense_variant c.1391C>T p.Pro464Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227422	snp	G	C	missense_variant c.1337C>G p.Pro446Arg	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227443	snp	G	C	missense_variant c.1316C>G p.Ala439Gly	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227452	snp	A	C	missense_variant c.1307T>G p.Leu436Arg	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227563	snp	G	A	missense_variant c.1196C>T p.Pro399Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227653	snp	A	G	missense_variant c.1106T>C p.Ile369Thr	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227668	snp	A	G	missense_variant c.1091T>C p.Val364Ala	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227818	snp	G	A	missense_variant c.941C>T p.Pro314Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227935	snp	T	A	missense_variant c.824A>T p.Asn275Ile	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227949	snp	A	C	missense_variant c.810T>G p.Ser270Arg	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228109	snp	C	G	missense_variant c.650G>C p.Arg217Pro	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228145	snp	C	T	missense_variant c.614G>A p.Cys205Tyr	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228151	snp	C	A	missense_variant c.608G>T p.Arg203Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228190	snp	G	A	missense_variant c.569C>T p.Ala190Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228265	snp	G	A	missense_variant c.494C>T p.Pro165Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228349	snp	G	A	missense_variant c.410C>T p.Ala137Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228397	snp	G	C	missense_variant c.362C>G p.Ala121Gly	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228433	snp	C	A	missense_variant c.326G>T p.Arg109Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228444	snp	T	G	missense_variant c.315A>C p.Arg105Ser	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228502	snp	C	T	missense_variant c.257G>A p.Ser86Asn	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228553	snp	G	T	missense_variant c.206C>A p.Pro69His	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2630356	snp	G	A	missense_variant c.31G>A p.Ala11Thr	yfgI	nalidixic acid resistance protein YfgI
2630599	snp	T	A	missense_variant c.274T>A p.Ser92Thr	yfgI	nalidixic acid resistance protein YfgI
3635277	snp	C	T	missense_variant c.437C>T p.Thr146Ile	yhiM	inner membrane protein with a role in acid resistance
3635534	snp	T	A	missense_variant c.694T>A p.Phe232Ile	yhiM	inner membrane protein with a role in acid resistance
3869635	snp	C	T	missense_variant c.259C>T p.Leu87Phe	cbrA	colicin M resistance protein
3869965	snp	T	G	missense_variant c.589T>G p.Ser197Ala	cbrA	colicin M resistance protein
3869974	snp	A	G	missense_variant c.598A>G p.Asn200Asp	cbrA	colicin M resistance protein
3870080	snp	G	A	missense_variant c.704G>A p.Ser235Asn	cbrA	colicin M resistance protein
3870253	snp	A	G	missense_variant c.877A>G p.Thr293Ala	cbrA	colicin M resistance protein
3870258	snp	C	G	missense_variant c.882C>G p.Asp294Glu	cbrA	colicin M resistance protein
4103121	snp	G	T	missense_variant c.300G>T p.Met100Ile	yiiM	2-amino-6-N-hydroxylaminopurine resistance protein

ID006

GenomePosition	Type	ReferenceAllele	AlternateAllele	Consequence	AffectedGene	Product
318076	snp	T	A	missense_variant c.244A>T p.Thr82Ser	rclC	reactive chlorine species resistance protein C
1620002	snp	C	T	missense_variant c.14C>T p.Ser5Leu	marB	multiple antibiotic resistance protein
1620058	snp	A	C	missense_variant c.70A>C p.Thr24Pro	marB	multiple antibiotic resistance protein
1620086	snp	C	G	missense_variant c.98C>G p.Ala33Gly	marB	multiple antibiotic resistance protein
2227335	snp	C	A	missense_variant c.1424G>T p.Gly475Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
3869815	snp	A	T	missense_variant c.439A>T p.Thr147Ser	cbrA	colicin M resistance protein
3869974	snp	A	G	missense_variant c.598A>G p.Asn200Asp	cbrA	colicin M resistance protein
3870106	snp	A	G	missense_variant c.730A>G p.Thr244Ala	cbrA	colicin M resistance protein
3870253	snp	A	G	missense_variant c.877A>G p.Thr293Ala	cbrA	colicin M resistance protein
3870258	snp	C	G	missense_variant c.882C>G p.Asp294Glu	cbrA	colicin M resistance protein
3870268	snp	T	G	missense_variant c.892T>G p.Ser298Ala	cbrA	colicin M resistance protein

ID007I

GenomePosition	Type	ReferenceAllele	AlternateAllele	Consequence	AffectedGene	Product
5732	snp	T	G	missense_variant c.728A>C p.Asp243Ala	yaaA	peroxide stress resistance protein YaaA
317780	snp	T	A	missense_variant c.540A>T p.Glu180Asp	rclC	reactive chlorine species resistance protein C
318312	snp	T	C	missense_variant c.8A>G p.Lys3Arg	rclC	reactive chlorine species resistance protein C
742927	snp	C	T	missense_variant c.101C>T p.Thr34Met	ybgI	radiation resistance protein YbgI
1006777	snp	G	C	missense_variant c.824C>G p.Ala275Gly	ycbX	6-N-hydroxylaminopurine resistance protein
1006933	snp	C	T	missense_variant c.668G>A p.Gly223Asp	ycbX	6-N-hydroxylaminopurine resistance protein
1007042	snp	G	T	missense_variant c.559C>A p.Arg187Ser	ycbX	6-N-hydroxylaminopurine resistance protein
1007131	snp	T	G	missense_variant c.470A>C p.Asp157Ala	ycbX	6-N-hydroxylaminopurine resistance protein
1007587	snp	A	G	missense_variant c.14T>C p.Ile5Thr	ycbX	6-N-hydroxylaminopurine resistance protein
1216402	snp	A	T	missense_variant c.34A>T p.Thr12Ser	ariR	regulator of acid resistance, influenced by indole
1216417	snp	G	T	missense_variant c.49G>T p.Ala17Ser	ariR	regulator of acid resistance, influenced by indole
1441685	snp	T	C	missense_variant c.59A>G p.Asn20Ser	hslJ	lipoprotein implicated in Novobiocin resistance
1441725	snp	A	G	missense_variant c.19T>C p.Phe7Leu	hslJ	lipoprotein implicated in Novobiocin resistance
1500741	snp	A	G	missense_variant c.169A>G p.Ser57Gly	tehA	tellurite resistance protein
1500753	snp	G	A	missense_variant c.181G>A p.Ala61Thr	tehA	tellurite resistance protein
1501299	snp	C	T	missense_variant c.727C>T p.Arg243Cys	tehA	tellurite resistance protein
1620002	snp	C	T	missense_variant c.14C>T p.Ser5Leu	marB	multiple antibiotic resistance protein
1620016	snp	G	A	missense_variant c.28G>A p.Ala10Thr	marB	multiple antibiotic resistance protein
1620086	snp	C	G	missense_variant c.98C>G p.Ala33Gly	marB	multiple antibiotic resistance protein
1620120	snp	C	A	missense_variant c.132C>A p.His44Gln	marB	multiple antibiotic resistance protein
2227335	snp	C	A	missense_variant c.1424G>T p.Gly475Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227452	snp	A	C	missense_variant c.1307T>G p.Leu436Arg	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227653	snp	A	G	missense_variant c.1106T>C p.Ile369Thr	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227818	snp	G	A	missense_variant c.941C>T p.Pro314Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227908	snp	G	A	missense_variant c.851C>T p.Ala284Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227935	snp	T	A	missense_variant c.824A>T p.Asn275Ile	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227949	snp	A	C	missense_variant c.810T>G p.Ser270Arg	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228109	snp	C	G	missense_variant c.650G>C p.Arg217Pro	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228145	snp	C	T	missense_variant c.614G>A p.Cys205Tyr	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228151	snp	C	A	missense_variant c.608G>T p.Arg203Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228241	snp	C	T	missense_variant c.518G>A p.Gly173Glu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228265	snp	G	A	missense_variant c.494C>T p.Pro165Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228277	snp	C	T	missense_variant c.482G>A p.Arg161Gln	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228349	snp	G	A	missense_variant c.410C>T p.Ala137Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228367	snp	C	A	missense_variant c.392G>T p.Arg131Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228397	snp	G	C	missense_variant c.362C>G p.Ala121Gly	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228406	snp	C	A	missense_variant c.353G>T p.Arg118Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228433	snp	C	A	missense_variant c.326G>T p.Arg109Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228463	snp	G	A	missense_variant c.296C>T p.Pro99Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2630599	snp	T	A	missense_variant c.274T>A p.Ser92Thr	yfgI	nalidixic acid resistance protein YfgI
3869965	snp	T	G	missense_variant c.589T>G p.Ser197Ala	cbrA	colicin M resistance protein
3869974	snp	A	G	missense_variant c.598A>G p.Asn200Asp	cbrA	colicin M resistance protein
3870106	snp	A	G	missense_variant c.730A>G p.Thr244Ala	cbrA	colicin M resistance protein
3870253	snp	A	G	missense_variant c.877A>G p.Thr293Ala	cbrA	colicin M resistance protein
3870258	snp	C	G	missense_variant c.882C>G p.Asp294Glu	cbrA	colicin M resistance protein
4102929	snp	G	C	missense_variant c.108G>C p.Glu36Asp	yiiM	2-amino-6-N-hydroxylaminopurine resistance protein

ID011

GenomePosition	Type	ReferenceAllele	AlternateAllele	Consequence	AffectedGene	Product
5732	snp	T	G	missense_variant c.728A>C p.Asp243Ala	yaaA	peroxide stress resistance protein YaaA
317780	snp	T	A	missense_variant c.540A>T p.Glu180Asp	rclC	reactive chlorine species resistance protein C
318312	snp	T	C	missense_variant c.8A>G p.Lys3Arg	rclC	reactive chlorine species resistance protein C
742927	snp	C	T	missense_variant c.101C>T p.Thr34Met	ybgI	radiation resistance protein YbgI
1006777	snp	G	C	missense_variant c.824C>G p.Ala275Gly	ycbX	6-N-hydroxylaminopurine resistance protein
1006933	snp	C	T	missense_variant c.668G>A p.Gly223Asp	ycbX	6-N-hydroxylaminopurine resistance protein
1007042	snp	G	T	missense_variant c.559C>A p.Arg187Ser	ycbX	6-N-hydroxylaminopurine resistance protein
1007131	snp	T	G	missense_variant c.470A>C p.Asp157Ala	ycbX	6-N-hydroxylaminopurine resistance protein
1007587	snp	A	G	missense_variant c.14T>C p.Ile5Thr	ycbX	6-N-hydroxylaminopurine resistance protein
1216402	snp	A	T	missense_variant c.34A>T p.Thr12Ser	ariR	regulator of acid resistance, influenced by indole
1216417	snp	G	T	missense_variant c.49G>T p.Ala17Ser	ariR	regulator of acid resistance, influenced by indole
1441685	snp	T	C	missense_variant c.59A>G p.Asn20Ser	hslJ	lipoprotein implicated in Novobiocin resistance
1441725	snp	A	G	missense_variant c.19T>C p.Phe7Leu	hslJ	lipoprotein implicated in Novobiocin resistance
1500741	snp	A	G	missense_variant c.169A>G p.Ser57Gly	tehA	tellurite resistance protein
1500753	snp	G	A	missense_variant c.181G>A p.Ala61Thr	tehA	tellurite resistance protein
1501299	snp	C	T	missense_variant c.727C>T p.Arg243Cys	tehA	tellurite resistance protein
1620002	snp	C	T	missense_variant c.14C>T p.Ser5Leu	marB	multiple antibiotic resistance protein
1620016	snp	G	A	missense_variant c.28G>A p.Ala10Thr	marB	multiple antibiotic resistance protein
1620086	snp	C	G	missense_variant c.98C>G p.Ala33Gly	marB	multiple antibiotic resistance protein
1620120	snp	C	A	missense_variant c.132C>A p.His44Gln	marB	multiple antibiotic resistance protein
2227335	snp	C	A	missense_variant c.1424G>T p.Gly475Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227452	snp	A	C	missense_variant c.1307T>G p.Leu436Arg	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227653	snp	A	G	missense_variant c.1106T>C p.Ile369Thr	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227818	snp	G	A	missense_variant c.941C>T p.Pro314Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227908	snp	G	A	missense_variant c.851C>T p.Ala284Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227935	snp	T	A	missense_variant c.824A>T p.Asn275Ile	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227949	snp	A	C	missense_variant c.810T>G p.Ser270Arg	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228109	snp	C	G	missense_variant c.650G>C p.Arg217Pro	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228145	snp	C	T	missense_variant c.614G>A p.Cys205Tyr	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228151	snp	C	A	missense_variant c.608G>T p.Arg203Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228241	snp	C	T	missense_variant c.518G>A p.Gly173Glu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228265	snp	G	A	missense_variant c.494C>T p.Pro165Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228277	snp	C	T	missense_variant c.482G>A p.Arg161Gln	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228349	snp	G	A	missense_variant c.410C>T p.Ala137Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228367	snp	C	A	missense_variant c.392G>T p.Arg131Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228397	snp	G	C	missense_variant c.362C>G p.Ala121Gly	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228406	snp	C	A	missense_variant c.353G>T p.Arg118Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228433	snp	C	A	missense_variant c.326G>T p.Arg109Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228463	snp	G	A	missense_variant c.296C>T p.Pro99Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2630395	snp	G	A	missense_variant c.70G>A p.Asp24Asn	yfgI	nalidixic acid resistance protein YfgI
2630599	snp	T	A	missense_variant c.274T>A p.Ser92Thr	yfgI	nalidixic acid resistance protein YfgI
3869965	snp	T	G	missense_variant c.589T>G p.Ser197Ala	cbrA	colicin M resistance protein
3869974	snp	A	G	missense_variant c.598A>G p.Asn200Asp	cbrA	colicin M resistance protein
3870106	snp	A	G	missense_variant c.730A>G p.Thr244Ala	cbrA	colicin M resistance protein
3870253	snp	A	G	missense_variant c.877A>G p.Thr293Ala	cbrA	colicin M resistance protein
3870258	snp	C	G	missense_variant c.882C>G p.Asp294Glu	cbrA	colicin M resistance protein
4102929	snp	G	C	missense_variant c.108G>C p.Glu36Asp	yiiM	2-amino-6-N-hydroxylaminopurine resistance protein

ID013I

GenomePosition	Type	ReferenceAllele	AlternateAllele	Consequence	AffectedGene	Product
5732	snp	T	G	missense_variant c.728A>C p.Asp243Ala	yaaA	peroxide stress resistance protein YaaA
317780	snp	T	A	missense_variant c.540A>T p.Glu180Asp	rclC	reactive chlorine species resistance protein C
318312	snp	T	C	missense_variant c.8A>G p.Lys3Arg	rclC	reactive chlorine species resistance protein C
742927	snp	C	T	missense_variant c.101C>T p.Thr34Met	ybgI	radiation resistance protein YbgI
1006777	snp	G	C	missense_variant c.824C>G p.Ala275Gly	ycbX	6-N-hydroxylaminopurine resistance protein
1006933	snp	C	T	missense_variant c.668G>A p.Gly223Asp	ycbX	6-N-hydroxylaminopurine resistance protein
1007042	snp	G	T	missense_variant c.559C>A p.Arg187Ser	ycbX	6-N-hydroxylaminopurine resistance protein
1007131	snp	T	G	missense_variant c.470A>C p.Asp157Ala	ycbX	6-N-hydroxylaminopurine resistance protein
1007587	snp	A	G	missense_variant c.14T>C p.Ile5Thr	ycbX	6-N-hydroxylaminopurine resistance protein
1216402	snp	A	T	missense_variant c.34A>T p.Thr12Ser	ariR	regulator of acid resistance, influenced by indole
1216417	snp	G	T	missense_variant c.49G>T p.Ala17Ser	ariR	regulator of acid resistance, influenced by indole
1441685	snp	T	C	missense_variant c.59A>G p.Asn20Ser	hslJ	lipoprotein implicated in Novobiocin resistance
1441725	snp	A	G	missense_variant c.19T>C p.Phe7Leu	hslJ	lipoprotein implicated in Novobiocin resistance
1500741	snp	A	G	missense_variant c.169A>G p.Ser57Gly	tehA	tellurite resistance protein
1500753	snp	G	A	missense_variant c.181G>A p.Ala61Thr	tehA	tellurite resistance protein
1501299	snp	C	T	missense_variant c.727C>T p.Arg243Cys	tehA	tellurite resistance protein
1620002	snp	C	T	missense_variant c.14C>T p.Ser5Leu	marB	multiple antibiotic resistance protein
1620016	snp	G	A	missense_variant c.28G>A p.Ala10Thr	marB	multiple antibiotic resistance protein
1620086	snp	C	G	missense_variant c.98C>G p.Ala33Gly	marB	multiple antibiotic resistance protein
1620120	snp	C	A	missense_variant c.132C>A p.His44Gln	marB	multiple antibiotic resistance protein
2227335	snp	C	A	missense_variant c.1424G>T p.Gly475Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227452	snp	A	C	missense_variant c.1307T>G p.Leu436Arg	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227653	snp	A	G	missense_variant c.1106T>C p.Ile369Thr	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227818	snp	G	A	missense_variant c.941C>T p.Pro314Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227908	snp	G	A	missense_variant c.851C>T p.Ala284Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227935	snp	T	A	missense_variant c.824A>T p.Asn275Ile	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227949	snp	A	C	missense_variant c.810T>G p.Ser270Arg	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228109	snp	C	G	missense_variant c.650G>C p.Arg217Pro	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228145	snp	C	T	missense_variant c.614G>A p.Cys205Tyr	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228151	snp	C	A	missense_variant c.608G>T p.Arg203Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228241	snp	C	T	missense_variant c.518G>A p.Gly173Glu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228265	snp	G	A	missense_variant c.494C>T p.Pro165Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228277	snp	C	T	missense_variant c.482G>A p.Arg161Gln	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228349	snp	G	A	missense_variant c.410C>T p.Ala137Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228367	snp	C	A	missense_variant c.392G>T p.Arg131Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228397	snp	G	C	missense_variant c.362C>G p.Ala121Gly	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228406	snp	C	A	missense_variant c.353G>T p.Arg118Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228433	snp	C	A	missense_variant c.326G>T p.Arg109Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228463	snp	G	A	missense_variant c.296C>T p.Pro99Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2630599	snp	T	A	missense_variant c.274T>A p.Ser92Thr	yfgI	nalidixic acid resistance protein YfgI
3869965	snp	T	G	missense_variant c.589T>G p.Ser197Ala	cbrA	colicin M resistance protein
3869974	snp	A	G	missense_variant c.598A>G p.Asn200Asp	cbrA	colicin M resistance protein
3870106	snp	A	G	missense_variant c.730A>G p.Thr244Ala	cbrA	colicin M resistance protein
3870253	snp	A	G	missense_variant c.877A>G p.Thr293Ala	cbrA	colicin M resistance protein
3870258	snp	C	G	missense_variant c.882C>G p.Asp294Glu	cbrA	colicin M resistance protein
4102929	snp	G	C	missense_variant c.108G>C p.Glu36Asp	yiiM	2-amino-6-N-hydroxylaminopurine resistance protein

ID016I

GenomePosition	Type	ReferenceAllele	AlternateAllele	Consequence	AffectedGene	Product
5732	snp	T	G	missense_variant c.728A>C p.Asp243Ala	yaaA	peroxide stress resistance protein YaaA
6162	snp	C	T	missense_variant c.298G>A p.Asp100Asn	yaaA	peroxide stress resistance protein YaaA
6239	snp	G	T	missense_variant c.221C>A p.Ala74Glu	yaaA	peroxide stress resistance protein YaaA
1007266	snp	C	T	missense_variant c.335G>A p.Gly112Glu	ycbX	6-N-hydroxylaminopurine resistance protein
2227335	snp	C	A	missense_variant c.1424G>T p.Gly475Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ

ID017

GenomePosition	Type	ReferenceAllele	AlternateAllele	Consequence	AffectedGene	Product
6239	snp	G	T	missense_variant c.221C>A p.Ala74Glu	yaaA	peroxide stress resistance protein YaaA
6401	snp	G	A	missense_variant c.59C>T p.Thr20Met	yaaA	peroxide stress resistance protein YaaA
317737	snp	T	C	missense_variant c.583A>G p.Thr195Ala	rclC	reactive chlorine species resistance protein C
318076	snp	T	A	missense_variant c.244A>T p.Thr82Ser	rclC	reactive chlorine species resistance protein C
318301	snp	G	T	missense_variant c.19C>A p.Leu7Met	rclC	reactive chlorine species resistance protein C
1007587	snp	A	G	missense_variant c.14T>C p.Ile5Thr	ycbX	6-N-hydroxylaminopurine resistance protein
1007596	snp	G	A	missense_variant c.5C>T p.Ala2Val	ycbX	6-N-hydroxylaminopurine resistance protein
1620120	snp	C	A	missense_variant c.132C>A p.His44Gln	marB	multiple antibiotic resistance protein
2227335	snp	C	A	missense_variant c.1424G>T p.Gly475Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227368	snp	G	A	missense_variant c.1391C>T p.Pro464Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227545	snp	C	A	missense_variant c.1214G>T p.Trp405Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228331	snp	A	T	missense_variant c.428T>A p.Val143Glu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228349	snp	G	A	missense_variant c.410C>T p.Ala137Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228433	snp	C	A	missense_variant c.326G>T p.Arg109Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228463	snp	G	A	missense_variant c.296C>T p.Pro99Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
3869713	snp	G	A	missense_variant c.337G>A p.Ala113Thr	cbrA	colicin M resistance protein
3869965	snp	T	G	missense_variant c.589T>G p.Ser197Ala	cbrA	colicin M resistance protein
3869974	snp	A	G	missense_variant c.598A>G p.Asn200Asp	cbrA	colicin M resistance protein
3870106	snp	A	G	missense_variant c.730A>G p.Thr244Ala	cbrA	colicin M resistance protein
3870253	snp	A	G	missense_variant c.877A>G p.Thr293Ala	cbrA	colicin M resistance protein
3870412	snp	G	A	missense_variant c.1036G>A p.Val346Met	cbrA	colicin M resistance protein
4103027	snp	C	T	missense_variant c.206C>T p.Ala69Val	yiiM	2-amino-6-N-hydroxylaminopurine resistance protein
4103116	snp	T	C	missense_variant c.295T>C p.Tyr99His	yiiM	2-amino-6-N-hydroxylaminopurine resistance protein

ID018CT

GenomePosition	Type	ReferenceAllele	AlternateAllele	Consequence	AffectedGene	Product
5732	snp	T	G	missense_variant c.728A>C p.Asp243Ala	yaaA	peroxide stress resistance protein YaaA
6239	snp	G	T	missense_variant c.221C>A p.Ala74Glu	yaaA	peroxide stress resistance protein YaaA
1007042	snp	G	T	missense_variant c.559C>A p.Arg187Ser	ycbX	6-N-hydroxylaminopurine resistance protein
1007587	snp	A	G	missense_variant c.14T>C p.Ile5Thr	ycbX	6-N-hydroxylaminopurine resistance protein
1216600	snp	G	A	missense_variant c.232G>A p.Glu78Lys	ariR	regulator of acid resistance, influenced by indole
1441685	snp	T	C	missense_variant c.59A>G p.Asn20Ser	hslJ	lipoprotein implicated in Novobiocin resistance
1441725	snp	A	G	missense_variant c.19T>C p.Phe7Leu	hslJ	lipoprotein implicated in Novobiocin resistance
1500753	snp	G	A	missense_variant c.181G>A p.Ala61Thr	tehA	tellurite resistance protein
1500807	snp	C	A	missense_variant c.235C>A p.Leu79Met	tehA	tellurite resistance protein
1501409	snp	T	A	missense_variant c.837T>A p.Asp279Glu	tehA	tellurite resistance protein
1620068	snp	C	T	missense_variant c.80C>T p.Pro27Leu	marB	multiple antibiotic resistance protein
1620120	snp	C	A	missense_variant c.132C>A p.His44Gln	marB	multiple antibiotic resistance protein
2227335	snp	C	A	missense_variant c.1424G>T p.Gly475Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228553	snp	G	T	missense_variant c.206C>A p.Pro69His	mdtQ	putative multidrug resistance outer membrane protein MdtQ
3635834	snp	G	A	missense_variant c.994G>A p.Val332Ile	yhiM	inner membrane protein with a role in acid resistance
3869407	snp	C	A	missense_variant c.31C>A p.Leu11Ile	cbrA	colicin M resistance protein
3869713	snp	G	A	missense_variant c.337G>A p.Ala113Thr	cbrA	colicin M resistance protein
3870106	snp	A	G	missense_variant c.730A>G p.Thr244Ala	cbrA	colicin M resistance protein
3870253	snp	A	G	missense_variant c.877A>G p.Thr293Ala	cbrA	colicin M resistance protein
3870268	snp	T	G	missense_variant c.892T>G p.Ser298Ala	cbrA	colicin M resistance protein
3870412	snp	G	A	missense_variant c.1036G>A p.Val346Met	cbrA	colicin M resistance protein

ID019

GenomePosition	Type	ReferenceAllele	AlternateAllele	Consequence	AffectedGene	Product
5732	snp	T	G	missense_variant c.728A>C p.Asp243Ala	yaaA	peroxide stress resistance protein YaaA
6239	snp	G	T	missense_variant c.221C>A p.Ala74Glu	yaaA	peroxide stress resistance protein YaaA
318076	snp	T	A	missense_variant c.244A>T p.Thr82Ser	rclC	reactive chlorine species resistance protein C
1216472	snp	G	T	missense_variant c.104G>T p.Gly35Val	ariR	regulator of acid resistance, influenced by indole
1216600	snp	G	A	missense_variant c.232G>A p.Glu78Lys	ariR	regulator of acid resistance, influenced by indole
1500753	snp	G	A	missense_variant c.181G>A p.Ala61Thr	tehA	tellurite resistance protein
1620068	snp	C	T	missense_variant c.80C>T p.Pro27Leu	marB	multiple antibiotic resistance protein
1620120	snp	C	A	missense_variant c.132C>A p.His44Gln	marB	multiple antibiotic resistance protein
2227335	snp	C	A	missense_variant c.1424G>T p.Gly475Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227368	snp	G	A	missense_variant c.1391C>T p.Pro464Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227545	snp	C	A	missense_variant c.1214G>T p.Trp405Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
3869407	snp	C	A	missense_variant c.31C>A p.Leu11Ile	cbrA	colicin M resistance protein
3869713	snp	G	A	missense_variant c.337G>A p.Ala113Thr	cbrA	colicin M resistance protein
3870106	snp	A	G	missense_variant c.730A>G p.Thr244Ala	cbrA	colicin M resistance protein
3870253	snp	A	G	missense_variant c.877A>G p.Thr293Ala	cbrA	colicin M resistance protein
3870268	snp	T	G	missense_variant c.892T>G p.Ser298Ala	cbrA	colicin M resistance protein
3870412	snp	G	A	missense_variant c.1036G>A p.Val346Met	cbrA	colicin M resistance protein
4103296	snp	C	A	missense_variant c.475C>A p.Pro159Thr	yiiM	2-amino-6-N-hydroxylaminopurine resistance protein

ID01CT

GenomePosition	Type	ReferenceAllele	AlternateAllele	Consequence	AffectedGene	Product
5732	snp	T	G	missense_variant c.728A>C p.Asp243Ala	yaaA	peroxide stress resistance protein YaaA
5877	snp	C	T	missense_variant c.583G>A p.Asp195Asn	yaaA	peroxide stress resistance protein YaaA
6239	snp	G	T	missense_variant c.221C>A p.Ala74Glu	yaaA	peroxide stress resistance protein YaaA
303486	snp	G	C	missense_variant c.496G>C p.Val166Leu	yagU	inner membrane protein that contributes to acid resistance
317823	snp	A	G	missense_variant c.497T>C p.Met166Thr	rclC	reactive chlorine species resistance protein C
1501490	snp	T	G	missense_variant c.918T>G p.Phe306Leu	tehA	tellurite resistance protein
1620068	snp	C	T	missense_variant c.80C>T p.Pro27Leu	marB	multiple antibiotic resistance protein
1620120	snp	C	A	missense_variant c.132C>A p.His44Gln	marB	multiple antibiotic resistance protein
2227335	snp	C	A	missense_variant c.1424G>T p.Gly475Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ

ID021

GenomePosition	Type	ReferenceAllele	AlternateAllele	Consequence	AffectedGene	Product
5732	snp	T	G	missense_variant c.728A>C p.Asp243Ala	yaaA	peroxide stress resistance protein YaaA
6162	snp	C	T	missense_variant c.298G>A p.Asp100Asn	yaaA	peroxide stress resistance protein YaaA
6239	snp	G	T	missense_variant c.221C>A p.Ala74Glu	yaaA	peroxide stress resistance protein YaaA
1007266	snp	C	T	missense_variant c.335G>A p.Gly112Glu	ycbX	6-N-hydroxylaminopurine resistance protein
2227335	snp	C	A	missense_variant c.1424G>T p.Gly475Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ

ID027

GenomePosition	Type	ReferenceAllele	AlternateAllele	Consequence	AffectedGene	Product
5732	snp	T	G	missense_variant c.728A>C p.Asp243Ala	yaaA	peroxide stress resistance protein YaaA
6162	snp	C	T	missense_variant c.298G>A p.Asp100Asn	yaaA	peroxide stress resistance protein YaaA
6239	snp	G	T	missense_variant c.221C>A p.Ala74Glu	yaaA	peroxide stress resistance protein YaaA
6288	snp	C	T	missense_variant c.172G>A p.Gly58Ser	yaaA	peroxide stress resistance protein YaaA
2227335	snp	C	A	missense_variant c.1424G>T p.Gly475Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ

ID031

GenomePosition	Type	ReferenceAllele	AlternateAllele	Consequence	AffectedGene	Product
6222	snp	T	C	missense_variant c.238A>G p.Ile80Val	yaaA	peroxide stress resistance protein YaaA
303486	snp	G	C	missense_variant c.496G>C p.Val166Leu	yagU	inner membrane protein that contributes to acid resistance
1501490	snp	T	G	missense_variant c.918T>G p.Phe306Leu	tehA	tellurite resistance protein
1620068	snp	C	T	missense_variant c.80C>T p.Pro27Leu	marB	multiple antibiotic resistance protein
1620120	snp	C	A	missense_variant c.132C>A p.His44Gln	marB	multiple antibiotic resistance protein
2227335	snp	C	A	missense_variant c.1424G>T p.Gly475Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227368	snp	G	A	missense_variant c.1391C>T p.Pro464Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227545	snp	C	A	missense_variant c.1214G>T p.Trp405Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228331	snp	A	T	missense_variant c.428T>A p.Val143Glu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228349	snp	G	A	missense_variant c.410C>T p.Ala137Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228433	snp	C	A	missense_variant c.326G>T p.Arg109Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228463	snp	G	A	missense_variant c.296C>T p.Pro99Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2630356	snp	G	A	missense_variant c.31G>A p.Ala11Thr	yfgI	nalidixic acid resistance protein YfgI

ID034I

GenomePosition	Type	ReferenceAllele	AlternateAllele	Consequence	AffectedGene	Product
5732	snp	T	G	missense_variant c.728A>C p.Asp243Ala	yaaA	peroxide stress resistance protein YaaA
6162	snp	C	T	missense_variant c.298G>A p.Asp100Asn	yaaA	peroxide stress resistance protein YaaA
6239	snp	G	T	missense_variant c.221C>A p.Ala74Glu	yaaA	peroxide stress resistance protein YaaA
1007266	snp	C	T	missense_variant c.335G>A p.Gly112Glu	ycbX	6-N-hydroxylaminopurine resistance protein
2227335	snp	C	A	missense_variant c.1424G>T p.Gly475Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
3635735	snp	T	A	missense_variant c.895T>A p.Cys299Ser	yhiM	inner membrane protein with a role in acid resistance

ID041

GenomePosition	Type	ReferenceAllele	AlternateAllele	Consequence	AffectedGene	Product
5732	snp	T	G	missense_variant c.728A>C p.Asp243Ala	yaaA	peroxide stress resistance protein YaaA
6239	snp	G	T	missense_variant c.221C>A p.Ala74Glu	yaaA	peroxide stress resistance protein YaaA
6408	snp	T	G	missense_variant c.52A>C p.Thr18Pro	yaaA	peroxide stress resistance protein YaaA
318076	snp	T	A	missense_variant c.244A>T p.Thr82Ser	rclC	reactive chlorine species resistance protein C
1006759	snp	G	A	missense_variant c.842C>T p.Ala281Val	ycbX	6-N-hydroxylaminopurine resistance protein
1007042	snp	G	T	missense_variant c.559C>A p.Arg187Ser	ycbX	6-N-hydroxylaminopurine resistance protein
1007587	snp	A	G	missense_variant c.14T>C p.Ile5Thr	ycbX	6-N-hydroxylaminopurine resistance protein
1216417	snp	G	T	missense_variant c.49G>T p.Ala17Ser	ariR	regulator of acid resistance, influenced by indole
1500753	snp	G	A	missense_variant c.181G>A p.Ala61Thr	tehA	tellurite resistance protein
1501407	snp	G	A	missense_variant c.835G>A p.Asp279Asn	tehA	tellurite resistance protein
1501518	snp	G	A	missense_variant c.946G>A p.Val316Ile	tehA	tellurite resistance protein
1620002	snp	C	T	missense_variant c.14C>T p.Ser5Leu	marB	multiple antibiotic resistance protein
1620022	snp	C	T	missense_variant c.34C>T p.Leu12Phe	marB	multiple antibiotic resistance protein
1620037	snp	G	A	missense_variant c.49G>A p.Ala17Thr	marB	multiple antibiotic resistance protein
1620046	snp	G	A	missense_variant c.58G>A p.Val20Ile	marB	multiple antibiotic resistance protein
1620120	snp	C	A	missense_variant c.132C>A p.His44Gln	marB	multiple antibiotic resistance protein
2227335	snp	C	A	missense_variant c.1424G>T p.Gly475Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227443	snp	G	C	missense_variant c.1316C>G p.Ala439Gly	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227452	snp	A	C	missense_variant c.1307T>G p.Leu436Arg	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227653	snp	A	G	missense_variant c.1106T>C p.Ile369Thr	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227872	snp	G	C	missense_variant c.887C>G p.Pro296Arg	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227926	snp	C	T	missense_variant c.833G>A p.Arg278His	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227949	snp	A	C	missense_variant c.810T>G p.Ser270Arg	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227968	snp	A	G	missense_variant c.791T>C p.Leu264Ser	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228265	snp	G	A	missense_variant c.494C>T p.Pro165Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228349	snp	G	A	missense_variant c.410C>T p.Ala137Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228397	snp	G	C	missense_variant c.362C>G p.Ala121Gly	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228433	snp	C	A	missense_variant c.326G>T p.Arg109Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228444	snp	T	G	missense_variant c.315A>C p.Arg105Ser	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228530	snp	T	C	missense_variant c.229A>G p.Thr77Ala	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228668	snp	C	T	missense_variant c.91G>A p.Ala31Thr	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2630821	snp	G	C	missense_variant c.496G>C p.Val166Leu	yfgI	nalidixic acid resistance protein YfgI
3635534	snp	T	A	missense_variant c.694T>A p.Phe232Ile	yhiM	inner membrane protein with a role in acid resistance
3869447	snp	G	A	missense_variant c.71G>A p.Gly24Asp	cbrA	colicin M resistance protein
3869965	snp	T	G	missense_variant c.589T>G p.Ser197Ala	cbrA	colicin M resistance protein
3869974	snp	A	G	missense_variant c.598A>G p.Asn200Asp	cbrA	colicin M resistance protein
3870080	snp	G	A	missense_variant c.704G>A p.Ser235Asn	cbrA	colicin M resistance protein
3870253	snp	A	G	missense_variant c.877A>G p.Thr293Ala	cbrA	colicin M resistance protein
3870258	snp	C	G	missense_variant c.882C>G p.Asp294Glu	cbrA	colicin M resistance protein
4102920	snp	G	A	missense_variant c.99G>A p.Met33Ile	yiiM	2-amino-6-N-hydroxylaminopurine resistance protein
4103121	snp	G	T	missense_variant c.300G>T p.Met100Ile	yiiM	2-amino-6-N-hydroxylaminopurine resistance protein

ID043I

GenomePosition	Type	ReferenceAllele	AlternateAllele	Consequence	AffectedGene	Product
5732	snp	T	G	missense_variant c.728A>C p.Asp243Ala	yaaA	peroxide stress resistance protein YaaA
6162	snp	C	T	missense_variant c.298G>A p.Asp100Asn	yaaA	peroxide stress resistance protein YaaA
6239	snp	G	T	missense_variant c.221C>A p.Ala74Glu	yaaA	peroxide stress resistance protein YaaA
6288	snp	C	T	missense_variant c.172G>A p.Gly58Ser	yaaA	peroxide stress resistance protein YaaA
1007266	snp	C	T	missense_variant c.335G>A p.Gly112Glu	ycbX	6-N-hydroxylaminopurine resistance protein
1216615	snp	T	A	missense_variant c.247T>A p.Tyr83Asn	ariR	regulator of acid resistance, influenced by indole
1500893	snp	C	G	missense_variant c.321C>G p.Cys107Trp	tehA	tellurite resistance protein
2227335	snp	C	A	missense_variant c.1424G>T p.Gly475Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2630545	snp	G	A	missense_variant c.220G>A p.Ala74Thr	yfgI	nalidixic acid resistance protein YfgI
2630629	snp	G	C	missense_variant c.304G>C p.Glu102Gln	yfgI	nalidixic acid resistance protein YfgI
3657346	snp	G	A	missense_variant c.352G>A p.Ala118Thr	hdeD	acid-resistance membrane protein

ID044

GenomePosition	Type	ReferenceAllele	AlternateAllele	Consequence	AffectedGene	Product
5732	snp	T	G	missense_variant c.728A>C p.Asp243Ala	yaaA	peroxide stress resistance protein YaaA
6162	snp	C	T	missense_variant c.298G>A p.Asp100Asn	yaaA	peroxide stress resistance protein YaaA
6239	snp	G	T	missense_variant c.221C>A p.Ala74Glu	yaaA	peroxide stress resistance protein YaaA
1007266	snp	C	T	missense_variant c.335G>A p.Gly112Glu	ycbX	6-N-hydroxylaminopurine resistance protein
2227335	snp	C	A	missense_variant c.1424G>T p.Gly475Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ

ID046II

GenomePosition	Type	ReferenceAllele	AlternateAllele	Consequence	AffectedGene	Product
5732	snp	T	G	missense_variant c.728A>C p.Asp243Ala	yaaA	peroxide stress resistance protein YaaA
6239	snp	G	T	missense_variant c.221C>A p.Ala74Glu	yaaA	peroxide stress resistance protein YaaA
2227335	snp	C	A	missense_variant c.1424G>T p.Gly475Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ

ID049

GenomePosition	Type	ReferenceAllele	AlternateAllele	Consequence	AffectedGene	Product
5732	snp	T	G	missense_variant c.728A>C p.Asp243Ala	yaaA	peroxide stress resistance protein YaaA
6239	snp	G	T	missense_variant c.221C>A p.Ala74Glu	yaaA	peroxide stress resistance protein YaaA
1169245	snp	C	T	missense_variant c.173C>T p.Ala58Val	bhsA	DUF1471 domain-containing multiple stress resistance outer membrane protein BhsA
1500924	snp	G	A	missense_variant c.352G>A p.Ala118Thr	tehA	tellurite resistance protein
1501490	snp	T	G	missense_variant c.918T>G p.Phe306Leu	tehA	tellurite resistance protein
1620068	snp	C	T	missense_variant c.80C>T p.Pro27Leu	marB	multiple antibiotic resistance protein
1620120	snp	C	A	missense_variant c.132C>A p.His44Gln	marB	multiple antibiotic resistance protein
2227335	snp	C	A	missense_variant c.1424G>T p.Gly475Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228422	snp	T	C	missense_variant c.337A>G p.Ser113Gly	mdtQ	putative multidrug resistance outer membrane protein MdtQ
3870196	snp	G	A	missense_variant c.820G>A p.Ala274Thr	cbrA	colicin M resistance protein

ID051

GenomePosition	Type	ReferenceAllele	AlternateAllele	Consequence	AffectedGene	Product
5732	snp	T	G	missense_variant c.728A>C p.Asp243Ala	yaaA	peroxide stress resistance protein YaaA
317780	snp	T	A	missense_variant c.540A>T p.Glu180Asp	rclC	reactive chlorine species resistance protein C
318312	snp	T	C	missense_variant c.8A>G p.Lys3Arg	rclC	reactive chlorine species resistance protein C
742927	snp	C	T	missense_variant c.101C>T p.Thr34Met	ybgI	radiation resistance protein YbgI
1006777	snp	G	C	missense_variant c.824C>G p.Ala275Gly	ycbX	6-N-hydroxylaminopurine resistance protein
1006933	snp	C	T	missense_variant c.668G>A p.Gly223Asp	ycbX	6-N-hydroxylaminopurine resistance protein
1007042	snp	G	T	missense_variant c.559C>A p.Arg187Ser	ycbX	6-N-hydroxylaminopurine resistance protein
1007131	snp	T	G	missense_variant c.470A>C p.Asp157Ala	ycbX	6-N-hydroxylaminopurine resistance protein
1007587	snp	A	G	missense_variant c.14T>C p.Ile5Thr	ycbX	6-N-hydroxylaminopurine resistance protein
1216402	snp	A	T	missense_variant c.34A>T p.Thr12Ser	ariR	regulator of acid resistance, influenced by indole
1216417	snp	G	T	missense_variant c.49G>T p.Ala17Ser	ariR	regulator of acid resistance, influenced by indole
1441685	snp	T	C	missense_variant c.59A>G p.Asn20Ser	hslJ	lipoprotein implicated in Novobiocin resistance
1441725	snp	A	G	missense_variant c.19T>C p.Phe7Leu	hslJ	lipoprotein implicated in Novobiocin resistance
1500741	snp	A	G	missense_variant c.169A>G p.Ser57Gly	tehA	tellurite resistance protein
1500753	snp	G	A	missense_variant c.181G>A p.Ala61Thr	tehA	tellurite resistance protein
1501299	snp	C	T	missense_variant c.727C>T p.Arg243Cys	tehA	tellurite resistance protein
1620002	snp	C	T	missense_variant c.14C>T p.Ser5Leu	marB	multiple antibiotic resistance protein
1620016	snp	G	A	missense_variant c.28G>A p.Ala10Thr	marB	multiple antibiotic resistance protein
1620086	snp	C	G	missense_variant c.98C>G p.Ala33Gly	marB	multiple antibiotic resistance protein
1620120	snp	C	A	missense_variant c.132C>A p.His44Gln	marB	multiple antibiotic resistance protein
2227335	snp	C	A	missense_variant c.1424G>T p.Gly475Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227452	snp	A	C	missense_variant c.1307T>G p.Leu436Arg	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227653	snp	A	G	missense_variant c.1106T>C p.Ile369Thr	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227818	snp	G	A	missense_variant c.941C>T p.Pro314Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227908	snp	G	A	missense_variant c.851C>T p.Ala284Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227935	snp	T	A	missense_variant c.824A>T p.Asn275Ile	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227949	snp	A	C	missense_variant c.810T>G p.Ser270Arg	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228109	snp	C	G	missense_variant c.650G>C p.Arg217Pro	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228145	snp	C	T	missense_variant c.614G>A p.Cys205Tyr	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228151	snp	C	A	missense_variant c.608G>T p.Arg203Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228241	snp	C	T	missense_variant c.518G>A p.Gly173Glu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228265	snp	G	A	missense_variant c.494C>T p.Pro165Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228277	snp	C	T	missense_variant c.482G>A p.Arg161Gln	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228349	snp	G	A	missense_variant c.410C>T p.Ala137Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228367	snp	C	A	missense_variant c.392G>T p.Arg131Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228397	snp	G	C	missense_variant c.362C>G p.Ala121Gly	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228406	snp	C	A	missense_variant c.353G>T p.Arg118Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228433	snp	C	A	missense_variant c.326G>T p.Arg109Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228463	snp	G	A	missense_variant c.296C>T p.Pro99Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2630599	snp	T	A	missense_variant c.274T>A p.Ser92Thr	yfgI	nalidixic acid resistance protein YfgI
3869965	snp	T	G	missense_variant c.589T>G p.Ser197Ala	cbrA	colicin M resistance protein
3869974	snp	A	G	missense_variant c.598A>G p.Asn200Asp	cbrA	colicin M resistance protein
3870106	snp	A	G	missense_variant c.730A>G p.Thr244Ala	cbrA	colicin M resistance protein
3870253	snp	A	G	missense_variant c.877A>G p.Thr293Ala	cbrA	colicin M resistance protein
3870258	snp	C	G	missense_variant c.882C>G p.Asp294Glu	cbrA	colicin M resistance protein
4102929	snp	G	C	missense_variant c.108G>C p.Glu36Asp	yiiM	2-amino-6-N-hydroxylaminopurine resistance protein

ID054

GenomePosition	Type	ReferenceAllele	AlternateAllele	Consequence	AffectedGene	Product
6239	snp	G	T	missense_variant c.221C>A p.Ala74Glu	yaaA	peroxide stress resistance protein YaaA
6401	snp	G	A	missense_variant c.59C>T p.Thr20Met	yaaA	peroxide stress resistance protein YaaA
317737	snp	T	C	missense_variant c.583A>G p.Thr195Ala	rclC	reactive chlorine species resistance protein C
318076	snp	T	A	missense_variant c.244A>T p.Thr82Ser	rclC	reactive chlorine species resistance protein C
318301	snp	G	T	missense_variant c.19C>A p.Leu7Met	rclC	reactive chlorine species resistance protein C
1007587	snp	A	G	missense_variant c.14T>C p.Ile5Thr	ycbX	6-N-hydroxylaminopurine resistance protein
1007596	snp	G	A	missense_variant c.5C>T p.Ala2Val	ycbX	6-N-hydroxylaminopurine resistance protein
1620120	snp	C	A	missense_variant c.132C>A p.His44Gln	marB	multiple antibiotic resistance protein
2227335	snp	C	A	missense_variant c.1424G>T p.Gly475Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227368	snp	G	A	missense_variant c.1391C>T p.Pro464Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227545	snp	C	A	missense_variant c.1214G>T p.Trp405Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228331	snp	A	T	missense_variant c.428T>A p.Val143Glu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228349	snp	G	A	missense_variant c.410C>T p.Ala137Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228433	snp	C	A	missense_variant c.326G>T p.Arg109Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228463	snp	G	A	missense_variant c.296C>T p.Pro99Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2630599	snp	T	A	missense_variant c.274T>A p.Ser92Thr	yfgI	nalidixic acid resistance protein YfgI
2630850	snp	C	A	missense_variant c.525C>A p.Asp175Glu	yfgI	nalidixic acid resistance protein YfgI
3869486	snp	G	A	missense_variant c.110G>A p.Cys37Tyr	cbrA	colicin M resistance protein
3869713	snp	G	A	missense_variant c.337G>A p.Ala113Thr	cbrA	colicin M resistance protein
3870106	snp	A	G	missense_variant c.730A>G p.Thr244Ala	cbrA	colicin M resistance protein
3870253	snp	A	G	missense_variant c.877A>G p.Thr293Ala	cbrA	colicin M resistance protein
3870268	snp	T	G	missense_variant c.892T>G p.Ser298Ala	cbrA	colicin M resistance protein
3870412	snp	G	A	missense_variant c.1036G>A p.Val346Met	cbrA	colicin M resistance protein
4103027	snp	C	T	missense_variant c.206C>T p.Ala69Val	yiiM	2-amino-6-N-hydroxylaminopurine resistance protein
4103116	snp	T	C	missense_variant c.295T>C p.Tyr99His	yiiM	2-amino-6-N-hydroxylaminopurine resistance protein

ID057

GenomePosition	Type	ReferenceAllele	AlternateAllele	Consequence	AffectedGene	Product
5732	snp	T	G	missense_variant c.728A>C p.Asp243Ala	yaaA	peroxide stress resistance protein YaaA
6239	snp	G	T	missense_variant c.221C>A p.Ala74Glu	yaaA	peroxide stress resistance protein YaaA
6401	snp	G	A	missense_variant c.59C>T p.Thr20Met	yaaA	peroxide stress resistance protein YaaA
318076	snp	T	A	missense_variant c.244A>T p.Thr82Ser	rclC	reactive chlorine species resistance protein C
1007587	snp	A	G	missense_variant c.14T>C p.Ile5Thr	ycbX	6-N-hydroxylaminopurine resistance protein
1500753	snp	G	A	missense_variant c.181G>A p.Ala61Thr	tehA	tellurite resistance protein
1620120	snp	C	A	missense_variant c.132C>A p.His44Gln	marB	multiple antibiotic resistance protein
2227335	snp	C	A	missense_variant c.1424G>T p.Gly475Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227368	snp	G	A	missense_variant c.1391C>T p.Pro464Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227545	snp	C	A	missense_variant c.1214G>T p.Trp405Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228331	snp	A	T	missense_variant c.428T>A p.Val143Glu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228349	snp	G	A	missense_variant c.410C>T p.Ala137Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228433	snp	C	A	missense_variant c.326G>T p.Arg109Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228463	snp	G	A	missense_variant c.296C>T p.Pro99Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2630450	snp	G	A	missense_variant c.125G>A p.Arg42Lys	yfgI	nalidixic acid resistance protein YfgI
3869713	snp	G	A	missense_variant c.337G>A p.Ala113Thr	cbrA	colicin M resistance protein
3869921	snp	C	T	missense_variant c.545C>T p.Ala182Val	cbrA	colicin M resistance protein
3870106	snp	A	G	missense_variant c.730A>G p.Thr244Ala	cbrA	colicin M resistance protein
3870253	snp	A	G	missense_variant c.877A>G p.Thr293Ala	cbrA	colicin M resistance protein
3870412	snp	G	A	missense_variant c.1036G>A p.Val346Met	cbrA	colicin M resistance protein

ID066II

GenomePosition	Type	ReferenceAllele	AlternateAllele	Consequence	AffectedGene	Product
5732	snp	T	G	missense_variant c.728A>C p.Asp243Ala	yaaA	peroxide stress resistance protein YaaA
6239	snp	G	T	missense_variant c.221C>A p.Ala74Glu	yaaA	peroxide stress resistance protein YaaA

ID067

GenomePosition	Type	ReferenceAllele	AlternateAllele	Consequence	AffectedGene	Product
5732	snp	T	G	missense_variant c.728A>C p.Asp243Ala	yaaA	peroxide stress resistance protein YaaA
6162	snp	C	T	missense_variant c.298G>A p.Asp100Asn	yaaA	peroxide stress resistance protein YaaA
6239	snp	G	T	missense_variant c.221C>A p.Ala74Glu	yaaA	peroxide stress resistance protein YaaA
6288	snp	C	T	missense_variant c.172G>A p.Gly58Ser	yaaA	peroxide stress resistance protein YaaA
1620002	snp	C	T	missense_variant c.14C>T p.Ser5Leu	marB	multiple antibiotic resistance protein
1620058	snp	A	C	missense_variant c.70A>C p.Thr24Pro	marB	multiple antibiotic resistance protein
1620086	snp	C	G	missense_variant c.98C>G p.Ala33Gly	marB	multiple antibiotic resistance protein
2227335	snp	C	A	missense_variant c.1424G>T p.Gly475Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228304	snp	A	C	missense_variant c.455T>G p.Ile152Ser	mdtQ	putative multidrug resistance outer membrane protein MdtQ
3657547	snp	T	A	missense_variant c.553T>A p.Leu185Met	hdeD	acid-resistance membrane protein
3869815	snp	A	T	missense_variant c.439A>T p.Thr147Ser	cbrA	colicin M resistance protein
3869974	snp	A	G	missense_variant c.598A>G p.Asn200Asp	cbrA	colicin M resistance protein
3870106	snp	A	G	missense_variant c.730A>G p.Thr244Ala	cbrA	colicin M resistance protein
3870253	snp	A	G	missense_variant c.877A>G p.Thr293Ala	cbrA	colicin M resistance protein
3870258	snp	C	G	missense_variant c.882C>G p.Asp294Glu	cbrA	colicin M resistance protein
3870268	snp	T	G	missense_variant c.892T>G p.Ser298Ala	cbrA	colicin M resistance protein

ID068

GenomePosition	Type	ReferenceAllele	AlternateAllele	Consequence	AffectedGene	Product
5732	snp	T	G	missense_variant c.728A>C p.Asp243Ala	yaaA	peroxide stress resistance protein YaaA
5756	snp	C	G	missense_variant c.704G>C p.Ser235Thr	yaaA	peroxide stress resistance protein YaaA
6239	snp	G	T	missense_variant c.221C>A p.Ala74Glu	yaaA	peroxide stress resistance protein YaaA
1007266	snp	C	T	missense_variant c.335G>A p.Gly112Glu	ycbX	6-N-hydroxylaminopurine resistance protein
2227335	snp	C	A	missense_variant c.1424G>T p.Gly475Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
3635735	snp	T	A	missense_variant c.895T>A p.Cys299Ser	yhiM	inner membrane protein with a role in acid resistance

ID073I

GenomePosition	Type	ReferenceAllele	AlternateAllele	Consequence	AffectedGene	Product
6162	snp	C	T	missense_variant c.298G>A p.Asp100Asn	yaaA	peroxide stress resistance protein YaaA
6239	snp	G	T	missense_variant c.221C>A p.Ala74Glu	yaaA	peroxide stress resistance protein YaaA
6288	snp	C	T	missense_variant c.172G>A p.Gly58Ser	yaaA	peroxide stress resistance protein YaaA
1620002	snp	C	T	missense_variant c.14C>T p.Ser5Leu	marB	multiple antibiotic resistance protein
1620058	snp	A	C	missense_variant c.70A>C p.Thr24Pro	marB	multiple antibiotic resistance protein
1620086	snp	C	G	missense_variant c.98C>G p.Ala33Gly	marB	multiple antibiotic resistance protein
2227335	snp	C	A	missense_variant c.1424G>T p.Gly475Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228304	snp	A	C	missense_variant c.455T>G p.Ile152Ser	mdtQ	putative multidrug resistance outer membrane protein MdtQ
3657547	snp	T	A	missense_variant c.553T>A p.Leu185Met	hdeD	acid-resistance membrane protein
3869815	snp	A	T	missense_variant c.439A>T p.Thr147Ser	cbrA	colicin M resistance protein
3869974	snp	A	G	missense_variant c.598A>G p.Asn200Asp	cbrA	colicin M resistance protein
3870106	snp	A	G	missense_variant c.730A>G p.Thr244Ala	cbrA	colicin M resistance protein
3870253	snp	A	G	missense_variant c.877A>G p.Thr293Ala	cbrA	colicin M resistance protein
3870258	snp	C	G	missense_variant c.882C>G p.Asp294Glu	cbrA	colicin M resistance protein
3870268	snp	T	G	missense_variant c.892T>G p.Ser298Ala	cbrA	colicin M resistance protein

ID077

GenomePosition	Type	ReferenceAllele	AlternateAllele	Consequence	AffectedGene	Product
6239	snp	G	T	missense_variant c.221C>A p.Ala74Glu	yaaA	peroxide stress resistance protein YaaA
6401	snp	G	A	missense_variant c.59C>T p.Thr20Met	yaaA	peroxide stress resistance protein YaaA
317737	snp	T	C	missense_variant c.583A>G p.Thr195Ala	rclC	reactive chlorine species resistance protein C
318076	snp	T	A	missense_variant c.244A>T p.Thr82Ser	rclC	reactive chlorine species resistance protein C
318301	snp	G	T	missense_variant c.19C>A p.Leu7Met	rclC	reactive chlorine species resistance protein C
1007587	snp	A	G	missense_variant c.14T>C p.Ile5Thr	ycbX	6-N-hydroxylaminopurine resistance protein
1007596	snp	G	A	missense_variant c.5C>T p.Ala2Val	ycbX	6-N-hydroxylaminopurine resistance protein
1620120	snp	C	A	missense_variant c.132C>A p.His44Gln	marB	multiple antibiotic resistance protein
2227335	snp	C	A	missense_variant c.1424G>T p.Gly475Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227368	snp	G	A	missense_variant c.1391C>T p.Pro464Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227545	snp	C	A	missense_variant c.1214G>T p.Trp405Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227822	snp	C	T	missense_variant c.937G>A p.Ala313Thr	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228331	snp	A	T	missense_variant c.428T>A p.Val143Glu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228349	snp	G	A	missense_variant c.410C>T p.Ala137Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228433	snp	C	A	missense_variant c.326G>T p.Arg109Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228463	snp	G	A	missense_variant c.296C>T p.Pro99Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2630599	snp	T	A	missense_variant c.274T>A p.Ser92Thr	yfgI	nalidixic acid resistance protein YfgI
2630850	snp	C	A	missense_variant c.525C>A p.Asp175Glu	yfgI	nalidixic acid resistance protein YfgI
3869486	snp	G	A	missense_variant c.110G>A p.Cys37Tyr	cbrA	colicin M resistance protein
3869713	snp	G	A	missense_variant c.337G>A p.Ala113Thr	cbrA	colicin M resistance protein
3870106	snp	A	G	missense_variant c.730A>G p.Thr244Ala	cbrA	colicin M resistance protein
3870253	snp	A	G	missense_variant c.877A>G p.Thr293Ala	cbrA	colicin M resistance protein
3870268	snp	T	G	missense_variant c.892T>G p.Ser298Ala	cbrA	colicin M resistance protein
3870412	snp	G	A	missense_variant c.1036G>A p.Val346Met	cbrA	colicin M resistance protein
4103027	snp	C	T	missense_variant c.206C>T p.Ala69Val	yiiM	2-amino-6-N-hydroxylaminopurine resistance protein
4103116	snp	T	C	missense_variant c.295T>C p.Tyr99His	yiiM	2-amino-6-N-hydroxylaminopurine resistance protein

ID081I

GenomePosition	Type	ReferenceAllele	AlternateAllele	Consequence	AffectedGene	Product
5732	snp	T	G	missense_variant c.728A>C p.Asp243Ala	yaaA	peroxide stress resistance protein YaaA
6239	snp	G	T	missense_variant c.221C>A p.Ala74Glu	yaaA	peroxide stress resistance protein YaaA
318076	snp	T	A	missense_variant c.244A>T p.Thr82Ser	rclC	reactive chlorine species resistance protein C
1441685	snp	T	C	missense_variant c.59A>G p.Asn20Ser	hslJ	lipoprotein implicated in Novobiocin resistance
1441725	snp	A	G	missense_variant c.19T>C p.Phe7Leu	hslJ	lipoprotein implicated in Novobiocin resistance
1620120	snp	C	A	missense_variant c.132C>A p.His44Gln	marB	multiple antibiotic resistance protein
2227335	snp	C	A	missense_variant c.1424G>T p.Gly475Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227476	snp	C	G	missense_variant c.1283G>C p.Arg428Pro	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228553	snp	G	T	missense_variant c.206C>A p.Pro69His	mdtQ	putative multidrug resistance outer membrane protein MdtQ
3635699	snp	T	A	missense_variant c.859T>A p.Leu287Ile	yhiM	inner membrane protein with a role in acid resistance
3869965	snp	T	G	missense_variant c.589T>G p.Ser197Ala	cbrA	colicin M resistance protein
3869974	snp	A	G	missense_variant c.598A>G p.Asn200Asp	cbrA	colicin M resistance protein
3870253	snp	A	G	missense_variant c.877A>G p.Thr293Ala	cbrA	colicin M resistance protein
4103338	snp	G	A	missense_variant c.517G>A p.Glu173Lys	yiiM	2-amino-6-N-hydroxylaminopurine resistance protein

ID086II

GenomePosition	Type	ReferenceAllele	AlternateAllele	Consequence	AffectedGene	Product
5732	snp	T	G	missense_variant c.728A>C p.Asp243Ala	yaaA	peroxide stress resistance protein YaaA
317780	snp	T	A	missense_variant c.540A>T p.Glu180Asp	rclC	reactive chlorine species resistance protein C
318312	snp	T	C	missense_variant c.8A>G p.Lys3Arg	rclC	reactive chlorine species resistance protein C
742927	snp	C	T	missense_variant c.101C>T p.Thr34Met	ybgI	radiation resistance protein YbgI
1006777	snp	G	C	missense_variant c.824C>G p.Ala275Gly	ycbX	6-N-hydroxylaminopurine resistance protein
1006933	snp	C	T	missense_variant c.668G>A p.Gly223Asp	ycbX	6-N-hydroxylaminopurine resistance protein
1007042	snp	G	T	missense_variant c.559C>A p.Arg187Ser	ycbX	6-N-hydroxylaminopurine resistance protein
1007131	snp	T	G	missense_variant c.470A>C p.Asp157Ala	ycbX	6-N-hydroxylaminopurine resistance protein
1007587	snp	A	G	missense_variant c.14T>C p.Ile5Thr	ycbX	6-N-hydroxylaminopurine resistance protein
1216402	snp	A	T	missense_variant c.34A>T p.Thr12Ser	ariR	regulator of acid resistance, influenced by indole
1216417	snp	G	T	missense_variant c.49G>T p.Ala17Ser	ariR	regulator of acid resistance, influenced by indole
1441685	snp	T	C	missense_variant c.59A>G p.Asn20Ser	hslJ	lipoprotein implicated in Novobiocin resistance
1441725	snp	A	G	missense_variant c.19T>C p.Phe7Leu	hslJ	lipoprotein implicated in Novobiocin resistance
1500741	snp	A	G	missense_variant c.169A>G p.Ser57Gly	tehA	tellurite resistance protein
1500753	snp	G	A	missense_variant c.181G>A p.Ala61Thr	tehA	tellurite resistance protein
1501299	snp	C	T	missense_variant c.727C>T p.Arg243Cys	tehA	tellurite resistance protein
1620002	snp	C	T	missense_variant c.14C>T p.Ser5Leu	marB	multiple antibiotic resistance protein
1620016	snp	G	A	missense_variant c.28G>A p.Ala10Thr	marB	multiple antibiotic resistance protein
1620086	snp	C	G	missense_variant c.98C>G p.Ala33Gly	marB	multiple antibiotic resistance protein
1620120	snp	C	A	missense_variant c.132C>A p.His44Gln	marB	multiple antibiotic resistance protein
2227335	snp	C	A	missense_variant c.1424G>T p.Gly475Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227452	snp	A	C	missense_variant c.1307T>G p.Leu436Arg	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227653	snp	A	G	missense_variant c.1106T>C p.Ile369Thr	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227818	snp	G	A	missense_variant c.941C>T p.Pro314Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227908	snp	G	A	missense_variant c.851C>T p.Ala284Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227935	snp	T	A	missense_variant c.824A>T p.Asn275Ile	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227949	snp	A	C	missense_variant c.810T>G p.Ser270Arg	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228109	snp	C	G	missense_variant c.650G>C p.Arg217Pro	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228145	snp	C	T	missense_variant c.614G>A p.Cys205Tyr	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228151	snp	C	A	missense_variant c.608G>T p.Arg203Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228241	snp	C	T	missense_variant c.518G>A p.Gly173Glu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228265	snp	G	A	missense_variant c.494C>T p.Pro165Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228277	snp	C	T	missense_variant c.482G>A p.Arg161Gln	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228349	snp	G	A	missense_variant c.410C>T p.Ala137Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228367	snp	C	A	missense_variant c.392G>T p.Arg131Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228397	snp	G	C	missense_variant c.362C>G p.Ala121Gly	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228406	snp	C	A	missense_variant c.353G>T p.Arg118Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228433	snp	C	A	missense_variant c.326G>T p.Arg109Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228463	snp	G	A	missense_variant c.296C>T p.Pro99Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2630599	snp	T	A	missense_variant c.274T>A p.Ser92Thr	yfgI	nalidixic acid resistance protein YfgI
3869965	snp	T	G	missense_variant c.589T>G p.Ser197Ala	cbrA	colicin M resistance protein
3869974	snp	A	G	missense_variant c.598A>G p.Asn200Asp	cbrA	colicin M resistance protein
3870106	snp	A	G	missense_variant c.730A>G p.Thr244Ala	cbrA	colicin M resistance protein
3870253	snp	A	G	missense_variant c.877A>G p.Thr293Ala	cbrA	colicin M resistance protein
3870258	snp	C	G	missense_variant c.882C>G p.Asp294Glu	cbrA	colicin M resistance protein
4102929	snp	G	C	missense_variant c.108G>C p.Glu36Asp	yiiM	2-amino-6-N-hydroxylaminopurine resistance protein

ID088

GenomePosition	Type	ReferenceAllele	AlternateAllele	Consequence	AffectedGene	Product
5732	snp	T	G	missense_variant c.728A>C p.Asp243Ala	yaaA	peroxide stress resistance protein YaaA
6162	snp	C	T	missense_variant c.298G>A p.Asp100Asn	yaaA	peroxide stress resistance protein YaaA
6239	snp	G	T	missense_variant c.221C>A p.Ala74Glu	yaaA	peroxide stress resistance protein YaaA
6288	snp	C	T	missense_variant c.172G>A p.Gly58Ser	yaaA	peroxide stress resistance protein YaaA
1007266	snp	C	T	missense_variant c.335G>A p.Gly112Glu	ycbX	6-N-hydroxylaminopurine resistance protein
1500893	snp	C	G	missense_variant c.321C>G p.Cys107Trp	tehA	tellurite resistance protein
2227335	snp	C	A	missense_variant c.1424G>T p.Gly475Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2630545	snp	G	A	missense_variant c.220G>A p.Ala74Thr	yfgI	nalidixic acid resistance protein YfgI
2630629	snp	G	C	missense_variant c.304G>C p.Glu102Gln	yfgI	nalidixic acid resistance protein YfgI

ID092

GenomePosition	Type	ReferenceAllele	AlternateAllele	Consequence	AffectedGene	Product
5732	snp	T	G	missense_variant c.728A>C p.Asp243Ala	yaaA	peroxide stress resistance protein YaaA
1007587	snp	A	G	missense_variant c.14T>C p.Ile5Thr	ycbX	6-N-hydroxylaminopurine resistance protein
1500753	snp	G	A	missense_variant c.181G>A p.Ala61Thr	tehA	tellurite resistance protein
1620120	snp	C	A	missense_variant c.132C>A p.His44Gln	marB	multiple antibiotic resistance protein
2227335	snp	C	A	missense_variant c.1424G>T p.Gly475Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227368	snp	G	A	missense_variant c.1391C>T p.Pro464Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227545	snp	C	A	missense_variant c.1214G>T p.Trp405Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228349	snp	G	A	missense_variant c.410C>T p.Ala137Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228433	snp	C	A	missense_variant c.326G>T p.Arg109Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
3870253	snp	A	G	missense_variant c.877A>G p.Thr293Ala	cbrA	colicin M resistance protein

ID094LLFII

GenomePosition	Type	ReferenceAllele	AlternateAllele	Consequence	AffectedGene	Product
5732	snp	T	G	missense_variant c.728A>C p.Asp243Ala	yaaA	peroxide stress resistance protein YaaA
6239	snp	G	T	missense_variant c.221C>A p.Ala74Glu	yaaA	peroxide stress resistance protein YaaA
1007587	snp	A	G	missense_variant c.14T>C p.Ile5Thr	ycbX	6-N-hydroxylaminopurine resistance protein
1500753	snp	G	A	missense_variant c.181G>A p.Ala61Thr	tehA	tellurite resistance protein
2227335	snp	C	A	missense_variant c.1424G>T p.Gly475Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ

ID099

GenomePosition	Type	ReferenceAllele	AlternateAllele	Consequence	AffectedGene	Product
6239	snp	G	T	missense_variant c.221C>A p.Ala74Glu	yaaA	peroxide stress resistance protein YaaA
6401	snp	G	A	missense_variant c.59C>T p.Thr20Met	yaaA	peroxide stress resistance protein YaaA
317737	snp	T	C	missense_variant c.583A>G p.Thr195Ala	rclC	reactive chlorine species resistance protein C
318076	snp	T	A	missense_variant c.244A>T p.Thr82Ser	rclC	reactive chlorine species resistance protein C
318301	snp	G	T	missense_variant c.19C>A p.Leu7Met	rclC	reactive chlorine species resistance protein C
1007587	snp	A	G	missense_variant c.14T>C p.Ile5Thr	ycbX	6-N-hydroxylaminopurine resistance protein
1007596	snp	G	A	missense_variant c.5C>T p.Ala2Val	ycbX	6-N-hydroxylaminopurine resistance protein
1620120	snp	C	A	missense_variant c.132C>A p.His44Gln	marB	multiple antibiotic resistance protein
2227335	snp	C	A	missense_variant c.1424G>T p.Gly475Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227368	snp	G	A	missense_variant c.1391C>T p.Pro464Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227545	snp	C	A	missense_variant c.1214G>T p.Trp405Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228331	snp	A	T	missense_variant c.428T>A p.Val143Glu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228349	snp	G	A	missense_variant c.410C>T p.Ala137Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228433	snp	C	A	missense_variant c.326G>T p.Arg109Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228463	snp	G	A	missense_variant c.296C>T p.Pro99Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
3869713	snp	G	A	missense_variant c.337G>A p.Ala113Thr	cbrA	colicin M resistance protein
3869965	snp	T	G	missense_variant c.589T>G p.Ser197Ala	cbrA	colicin M resistance protein
3869974	snp	A	G	missense_variant c.598A>G p.Asn200Asp	cbrA	colicin M resistance protein
3870106	snp	A	G	missense_variant c.730A>G p.Thr244Ala	cbrA	colicin M resistance protein
3870253	snp	A	G	missense_variant c.877A>G p.Thr293Ala	cbrA	colicin M resistance protein
3870412	snp	G	A	missense_variant c.1036G>A p.Val346Met	cbrA	colicin M resistance protein
4103027	snp	C	T	missense_variant c.206C>T p.Ala69Val	yiiM	2-amino-6-N-hydroxylaminopurine resistance protein
4103116	snp	T	C	missense_variant c.295T>C p.Tyr99His	yiiM	2-amino-6-N-hydroxylaminopurine resistance protein

ID09CT

GenomePosition	Type	ReferenceAllele	AlternateAllele	Consequence	AffectedGene	Product
6239	snp	G	T	missense_variant c.221C>A p.Ala74Glu	yaaA	peroxide stress resistance protein YaaA
1007042	snp	G	T	missense_variant c.559C>A p.Arg187Ser	ycbX	6-N-hydroxylaminopurine resistance protein
1007587	snp	A	G	missense_variant c.14T>C p.Ile5Thr	ycbX	6-N-hydroxylaminopurine resistance protein
1441604	snp	C	T	missense_variant c.140G>A p.Ser47Asn	hslJ	lipoprotein implicated in Novobiocin resistance
1500753	snp	G	A	missense_variant c.181G>A p.Ala61Thr	tehA	tellurite resistance protein
1620120	snp	C	A	missense_variant c.132C>A p.His44Gln	marB	multiple antibiotic resistance protein
2227335	snp	C	A	missense_variant c.1424G>T p.Gly475Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227368	snp	G	A	missense_variant c.1391C>T p.Pro464Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227545	snp	C	A	missense_variant c.1214G>T p.Trp405Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228331	snp	A	T	missense_variant c.428T>A p.Val143Glu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228349	snp	G	A	missense_variant c.410C>T p.Ala137Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228433	snp	C	A	missense_variant c.326G>T p.Arg109Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228463	snp	G	A	missense_variant c.296C>T p.Pro99Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228556	snp	A	C	missense_variant c.203T>G p.Leu68Arg	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2630599	snp	T	A	missense_variant c.274T>A p.Ser92Thr	yfgI	nalidixic acid resistance protein YfgI
2630850	snp	C	A	missense_variant c.525C>A p.Asp175Glu	yfgI	nalidixic acid resistance protein YfgI
3870106	snp	A	G	missense_variant c.730A>G p.Thr244Ala	cbrA	colicin M resistance protein
3870253	snp	A	G	missense_variant c.877A>G p.Thr293Ala	cbrA	colicin M resistance protein
3870412	snp	G	A	missense_variant c.1036G>A p.Val346Met	cbrA	colicin M resistance protein

ID101

GenomePosition	Type	ReferenceAllele	AlternateAllele	Consequence	AffectedGene	Product
6239	snp	G	T	missense_variant c.221C>A p.Ala74Glu	yaaA	peroxide stress resistance protein YaaA
6401	snp	G	A	missense_variant c.59C>T p.Thr20Met	yaaA	peroxide stress resistance protein YaaA
317737	snp	T	C	missense_variant c.583A>G p.Thr195Ala	rclC	reactive chlorine species resistance protein C
318076	snp	T	A	missense_variant c.244A>T p.Thr82Ser	rclC	reactive chlorine species resistance protein C
318301	snp	G	T	missense_variant c.19C>A p.Leu7Met	rclC	reactive chlorine species resistance protein C
1007587	snp	A	G	missense_variant c.14T>C p.Ile5Thr	ycbX	6-N-hydroxylaminopurine resistance protein
1007596	snp	G	A	missense_variant c.5C>T p.Ala2Val	ycbX	6-N-hydroxylaminopurine resistance protein
1620120	snp	C	A	missense_variant c.132C>A p.His44Gln	marB	multiple antibiotic resistance protein
2227335	snp	C	A	missense_variant c.1424G>T p.Gly475Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227368	snp	G	A	missense_variant c.1391C>T p.Pro464Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227545	snp	C	A	missense_variant c.1214G>T p.Trp405Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228331	snp	A	T	missense_variant c.428T>A p.Val143Glu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228349	snp	G	A	missense_variant c.410C>T p.Ala137Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228433	snp	C	A	missense_variant c.326G>T p.Arg109Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228463	snp	G	A	missense_variant c.296C>T p.Pro99Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
3869713	snp	G	A	missense_variant c.337G>A p.Ala113Thr	cbrA	colicin M resistance protein
3869965	snp	T	G	missense_variant c.589T>G p.Ser197Ala	cbrA	colicin M resistance protein
3869974	snp	A	G	missense_variant c.598A>G p.Asn200Asp	cbrA	colicin M resistance protein
3870106	snp	A	G	missense_variant c.730A>G p.Thr244Ala	cbrA	colicin M resistance protein
3870253	snp	A	G	missense_variant c.877A>G p.Thr293Ala	cbrA	colicin M resistance protein
3870412	snp	G	A	missense_variant c.1036G>A p.Val346Met	cbrA	colicin M resistance protein
4103027	snp	C	T	missense_variant c.206C>T p.Ala69Val	yiiM	2-amino-6-N-hydroxylaminopurine resistance protein
4103116	snp	T	C	missense_variant c.295T>C p.Tyr99His	yiiM	2-amino-6-N-hydroxylaminopurine resistance protein

ID107II

GenomePosition	Type	ReferenceAllele	AlternateAllele	Consequence	AffectedGene	Product
5732	snp	T	G	missense_variant c.728A>C p.Asp243Ala	yaaA	peroxide stress resistance protein YaaA
6408	snp	T	G	missense_variant c.52A>C p.Thr18Pro	yaaA	peroxide stress resistance protein YaaA
317780	snp	T	A	missense_variant c.540A>T p.Glu180Asp	rclC	reactive chlorine species resistance protein C
318076	snp	T	A	missense_variant c.244A>T p.Thr82Ser	rclC	reactive chlorine species resistance protein C
1007042	snp	G	T	missense_variant c.559C>A p.Arg187Ser	ycbX	6-N-hydroxylaminopurine resistance protein
1007428	snp	G	A	missense_variant c.173C>T p.Thr58Ile	ycbX	6-N-hydroxylaminopurine resistance protein
1007587	snp	A	G	missense_variant c.14T>C p.Ile5Thr	ycbX	6-N-hydroxylaminopurine resistance protein
1216402	snp	A	G	missense_variant c.34A>G p.Thr12Ala	ariR	regulator of acid resistance, influenced by indole
1216417	snp	G	T	missense_variant c.49G>T p.Ala17Ser	ariR	regulator of acid resistance, influenced by indole
1216562	snp	G	A	missense_variant c.194G>A p.Ser65Asn	ariR	regulator of acid resistance, influenced by indole
1500615	snp	G	A	missense_variant c.43G>A p.Gly15Ser	tehA	tellurite resistance protein
1500741	snp	A	G	missense_variant c.169A>G p.Ser57Gly	tehA	tellurite resistance protein
1500753	snp	G	A	missense_variant c.181G>A p.Ala61Thr	tehA	tellurite resistance protein
1501399	snp	G	T	missense_variant c.827G>T p.Ser276Ile	tehA	tellurite resistance protein
1501518	snp	G	A	missense_variant c.946G>A p.Val316Ile	tehA	tellurite resistance protein
1620002	snp	C	T	missense_variant c.14C>T p.Ser5Leu	marB	multiple antibiotic resistance protein
1620120	snp	C	A	missense_variant c.132C>A p.His44Gln	marB	multiple antibiotic resistance protein
2227335	snp	C	A	missense_variant c.1424G>T p.Gly475Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227353	snp	A	G	missense_variant c.1406T>C p.Leu469Pro	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227510	snp	C	T	missense_variant c.1249G>A p.Ala417Thr	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227560	snp	A	G	missense_variant c.1199T>C p.Val400Ala	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227566	snp	T	C	missense_variant c.1193A>G p.Gln398Arg	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227653	snp	A	G	missense_variant c.1106T>C p.Ile369Thr	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227872	snp	G	C	missense_variant c.887C>G p.Pro296Arg	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227935	snp	T	A	missense_variant c.824A>T p.Asn275Ile	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227949	snp	A	C	missense_variant c.810T>G p.Ser270Arg	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228109	snp	C	G	missense_variant c.650G>C p.Arg217Pro	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228239	snp	G	A	missense_variant c.520C>T p.Arg174Trp	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228265	snp	G	A	missense_variant c.494C>T p.Pro165Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228349	snp	G	A	missense_variant c.410C>T p.Ala137Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228367	snp	C	A	missense_variant c.392G>T p.Arg131Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228397	snp	G	C	missense_variant c.362C>G p.Ala121Gly	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228433	snp	C	A	missense_variant c.326G>T p.Arg109Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2630364	snp	A	T	missense_variant c.39A>T p.Leu13Phe	yfgI	nalidixic acid resistance protein YfgI
2630599	snp	T	A	missense_variant c.274T>A p.Ser92Thr	yfgI	nalidixic acid resistance protein YfgI
3635534	snp	T	A	missense_variant c.694T>A p.Phe232Ile	yhiM	inner membrane protein with a role in acid resistance
3635595	snp	C	T	missense_variant c.755C>T p.Ala252Val	yhiM	inner membrane protein with a role in acid resistance
3869965	snp	T	G	missense_variant c.589T>G p.Ser197Ala	cbrA	colicin M resistance protein
3869974	snp	A	G	missense_variant c.598A>G p.Asn200Asp	cbrA	colicin M resistance protein
3870080	snp	G	A	missense_variant c.704G>A p.Ser235Asn	cbrA	colicin M resistance protein
3870253	snp	A	G	missense_variant c.877A>G p.Thr293Ala	cbrA	colicin M resistance protein
3870258	snp	C	G	missense_variant c.882C>G p.Asp294Glu	cbrA	colicin M resistance protein
3870295	snp	C	A	missense_variant c.919C>A p.Leu307Ile	cbrA	colicin M resistance protein
4102964	snp	A	T	missense_variant c.143A>T p.Lys48Met	yiiM	2-amino-6-N-hydroxylaminopurine resistance protein

ID124

GenomePosition	Type	ReferenceAllele	AlternateAllele	Consequence	AffectedGene	Product
5732	snp	T	G	missense_variant c.728A>C p.Asp243Ala	yaaA	peroxide stress resistance protein YaaA
6162	snp	C	T	missense_variant c.298G>A p.Asp100Asn	yaaA	peroxide stress resistance protein YaaA
6239	snp	G	T	missense_variant c.221C>A p.Ala74Glu	yaaA	peroxide stress resistance protein YaaA
1007266	snp	C	T	missense_variant c.335G>A p.Gly112Glu	ycbX	6-N-hydroxylaminopurine resistance protein
2227335	snp	C	A	missense_variant c.1424G>T p.Gly475Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228170	snp	G	A	missense_variant c.589C>T p.Pro197Ser	mdtQ	putative multidrug resistance outer membrane protein MdtQ

ID127

GenomePosition	Type	ReferenceAllele	AlternateAllele	Consequence	AffectedGene	Product
5732	snp	T	G	missense_variant c.728A>C p.Asp243Ala	yaaA	peroxide stress resistance protein YaaA
6162	snp	C	T	missense_variant c.298G>A p.Asp100Asn	yaaA	peroxide stress resistance protein YaaA
6239	snp	G	T	missense_variant c.221C>A p.Ala74Glu	yaaA	peroxide stress resistance protein YaaA
1007266	snp	C	T	missense_variant c.335G>A p.Gly112Glu	ycbX	6-N-hydroxylaminopurine resistance protein
2227335	snp	C	A	missense_variant c.1424G>T p.Gly475Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ

ID128

GenomePosition	Type	ReferenceAllele	AlternateAllele	Consequence	AffectedGene	Product
5732	snp	T	G	missense_variant c.728A>C p.Asp243Ala	yaaA	peroxide stress resistance protein YaaA
317780	snp	T	A	missense_variant c.540A>T p.Glu180Asp	rclC	reactive chlorine species resistance protein C
318312	snp	T	C	missense_variant c.8A>G p.Lys3Arg	rclC	reactive chlorine species resistance protein C
742927	snp	C	T	missense_variant c.101C>T p.Thr34Met	ybgI	radiation resistance protein YbgI
1006777	snp	G	C	missense_variant c.824C>G p.Ala275Gly	ycbX	6-N-hydroxylaminopurine resistance protein
1006933	snp	C	T	missense_variant c.668G>A p.Gly223Asp	ycbX	6-N-hydroxylaminopurine resistance protein
1007042	snp	G	T	missense_variant c.559C>A p.Arg187Ser	ycbX	6-N-hydroxylaminopurine resistance protein
1007131	snp	T	G	missense_variant c.470A>C p.Asp157Ala	ycbX	6-N-hydroxylaminopurine resistance protein
1007587	snp	A	G	missense_variant c.14T>C p.Ile5Thr	ycbX	6-N-hydroxylaminopurine resistance protein
1216402	snp	A	T	missense_variant c.34A>T p.Thr12Ser	ariR	regulator of acid resistance, influenced by indole
1216417	snp	G	T	missense_variant c.49G>T p.Ala17Ser	ariR	regulator of acid resistance, influenced by indole
1441685	snp	T	C	missense_variant c.59A>G p.Asn20Ser	hslJ	lipoprotein implicated in Novobiocin resistance
1441725	snp	A	G	missense_variant c.19T>C p.Phe7Leu	hslJ	lipoprotein implicated in Novobiocin resistance
1500741	snp	A	G	missense_variant c.169A>G p.Ser57Gly	tehA	tellurite resistance protein
1500753	snp	G	A	missense_variant c.181G>A p.Ala61Thr	tehA	tellurite resistance protein
1501299	snp	C	T	missense_variant c.727C>T p.Arg243Cys	tehA	tellurite resistance protein
1620002	snp	C	T	missense_variant c.14C>T p.Ser5Leu	marB	multiple antibiotic resistance protein
1620016	snp	G	A	missense_variant c.28G>A p.Ala10Thr	marB	multiple antibiotic resistance protein
1620086	snp	C	G	missense_variant c.98C>G p.Ala33Gly	marB	multiple antibiotic resistance protein
1620120	snp	C	A	missense_variant c.132C>A p.His44Gln	marB	multiple antibiotic resistance protein
2227335	snp	C	A	missense_variant c.1424G>T p.Gly475Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227452	snp	A	C	missense_variant c.1307T>G p.Leu436Arg	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227653	snp	A	G	missense_variant c.1106T>C p.Ile369Thr	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227818	snp	G	A	missense_variant c.941C>T p.Pro314Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227908	snp	G	A	missense_variant c.851C>T p.Ala284Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227935	snp	T	A	missense_variant c.824A>T p.Asn275Ile	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227949	snp	A	C	missense_variant c.810T>G p.Ser270Arg	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228109	snp	C	G	missense_variant c.650G>C p.Arg217Pro	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228145	snp	C	T	missense_variant c.614G>A p.Cys205Tyr	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228151	snp	C	A	missense_variant c.608G>T p.Arg203Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228241	snp	C	T	missense_variant c.518G>A p.Gly173Glu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228265	snp	G	A	missense_variant c.494C>T p.Pro165Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228277	snp	C	T	missense_variant c.482G>A p.Arg161Gln	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228349	snp	G	A	missense_variant c.410C>T p.Ala137Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228367	snp	C	A	missense_variant c.392G>T p.Arg131Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228397	snp	G	C	missense_variant c.362C>G p.Ala121Gly	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228406	snp	C	A	missense_variant c.353G>T p.Arg118Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228433	snp	C	A	missense_variant c.326G>T p.Arg109Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228463	snp	G	A	missense_variant c.296C>T p.Pro99Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2630599	snp	T	A	missense_variant c.274T>A p.Ser92Thr	yfgI	nalidixic acid resistance protein YfgI
3869965	snp	T	G	missense_variant c.589T>G p.Ser197Ala	cbrA	colicin M resistance protein
3869974	snp	A	G	missense_variant c.598A>G p.Asn200Asp	cbrA	colicin M resistance protein
3870106	snp	A	G	missense_variant c.730A>G p.Thr244Ala	cbrA	colicin M resistance protein
3870253	snp	A	G	missense_variant c.877A>G p.Thr293Ala	cbrA	colicin M resistance protein
3870258	snp	C	G	missense_variant c.882C>G p.Asp294Glu	cbrA	colicin M resistance protein
4102929	snp	G	C	missense_variant c.108G>C p.Glu36Asp	yiiM	2-amino-6-N-hydroxylaminopurine resistance protein

ID129E

GenomePosition	Type	ReferenceAllele	AlternateAllele	Consequence	AffectedGene	Product
5732	snp	T	G	missense_variant c.728A>C p.Asp243Ala	yaaA	peroxide stress resistance protein YaaA
6239	snp	G	T	missense_variant c.221C>A p.Ala74Glu	yaaA	peroxide stress resistance protein YaaA
318076	snp	T	A	missense_variant c.244A>T p.Thr82Ser	rclC	reactive chlorine species resistance protein C
318301	snp	G	T	missense_variant c.19C>A p.Leu7Met	rclC	reactive chlorine species resistance protein C
1007042	snp	G	T	missense_variant c.559C>A p.Arg187Ser	ycbX	6-N-hydroxylaminopurine resistance protein
1007587	snp	A	G	missense_variant c.14T>C p.Ile5Thr	ycbX	6-N-hydroxylaminopurine resistance protein
1007596	snp	G	A	missense_variant c.5C>T p.Ala2Val	ycbX	6-N-hydroxylaminopurine resistance protein
1441604	snp	C	T	missense_variant c.140G>A p.Ser47Asn	hslJ	lipoprotein implicated in Novobiocin resistance
1500753	snp	G	A	missense_variant c.181G>A p.Ala61Thr	tehA	tellurite resistance protein
1500807	snp	C	A	missense_variant c.235C>A p.Leu79Met	tehA	tellurite resistance protein
1620120	snp	C	A	missense_variant c.132C>A p.His44Gln	marB	multiple antibiotic resistance protein
2227335	snp	C	A	missense_variant c.1424G>T p.Gly475Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227368	snp	G	A	missense_variant c.1391C>T p.Pro464Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227545	snp	C	A	missense_variant c.1214G>T p.Trp405Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228331	snp	A	T	missense_variant c.428T>A p.Val143Glu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228349	snp	G	A	missense_variant c.410C>T p.Ala137Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228433	snp	C	A	missense_variant c.326G>T p.Arg109Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228463	snp	G	A	missense_variant c.296C>T p.Pro99Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
3869713	snp	G	A	missense_variant c.337G>A p.Ala113Thr	cbrA	colicin M resistance protein
3870106	snp	A	G	missense_variant c.730A>G p.Thr244Ala	cbrA	colicin M resistance protein
3870253	snp	A	G	missense_variant c.877A>G p.Thr293Ala	cbrA	colicin M resistance protein
3870268	snp	T	G	missense_variant c.892T>G p.Ser298Ala	cbrA	colicin M resistance protein
3870412	snp	G	A	missense_variant c.1036G>A p.Val346Met	cbrA	colicin M resistance protein
4103296	snp	C	A	missense_variant c.475C>A p.Pro159Thr	yiiM	2-amino-6-N-hydroxylaminopurine resistance protein

ID130

GenomePosition	Type	ReferenceAllele	AlternateAllele	Consequence	AffectedGene	Product
5732	snp	T	G	missense_variant c.728A>C p.Asp243Ala	yaaA	peroxide stress resistance protein YaaA
6162	snp	C	T	missense_variant c.298G>A p.Asp100Asn	yaaA	peroxide stress resistance protein YaaA
6239	snp	G	T	missense_variant c.221C>A p.Ala74Glu	yaaA	peroxide stress resistance protein YaaA
742927	snp	C	A	missense_variant c.101C>A p.Thr34Lys	ybgI	radiation resistance protein YbgI
1007042	snp	G	T	missense_variant c.559C>A p.Arg187Ser	ycbX	6-N-hydroxylaminopurine resistance protein
1007111	snp	C	T	missense_variant c.490G>A p.Ala164Thr	ycbX	6-N-hydroxylaminopurine resistance protein
1007587	snp	A	G	missense_variant c.14T>C p.Ile5Thr	ycbX	6-N-hydroxylaminopurine resistance protein
1500753	snp	G	A	missense_variant c.181G>A p.Ala61Thr	tehA	tellurite resistance protein
1620120	snp	C	A	missense_variant c.132C>A p.His44Gln	marB	multiple antibiotic resistance protein
2227335	snp	C	A	missense_variant c.1424G>T p.Gly475Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228553	snp	G	T	missense_variant c.206C>A p.Pro69His	mdtQ	putative multidrug resistance outer membrane protein MdtQ
3869407	snp	C	A	missense_variant c.31C>A p.Leu11Ile	cbrA	colicin M resistance protein
3869713	snp	G	A	missense_variant c.337G>A p.Ala113Thr	cbrA	colicin M resistance protein
3870106	snp	A	G	missense_variant c.730A>G p.Thr244Ala	cbrA	colicin M resistance protein
3870253	snp	A	G	missense_variant c.877A>G p.Thr293Ala	cbrA	colicin M resistance protein
3870268	snp	T	G	missense_variant c.892T>G p.Ser298Ala	cbrA	colicin M resistance protein
3870346	snp	G	A	missense_variant c.970G>A p.Gly324Ser	cbrA	colicin M resistance protein
3870412	snp	G	A	missense_variant c.1036G>A p.Val346Met	cbrA	colicin M resistance protein

ID134

GenomePosition	Type	ReferenceAllele	AlternateAllele	Consequence	AffectedGene	Product
5732	snp	T	G	missense_variant c.728A>C p.Asp243Ala	yaaA	peroxide stress resistance protein YaaA
6239	snp	G	T	missense_variant c.221C>A p.Ala74Glu	yaaA	peroxide stress resistance protein YaaA
2227335	snp	C	A	missense_variant c.1424G>T p.Gly475Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ

ID136

GenomePosition	Type	ReferenceAllele	AlternateAllele	Consequence	AffectedGene	Product
6239	snp	G	T	missense_variant c.221C>A p.Ala74Glu	yaaA	peroxide stress resistance protein YaaA
6401	snp	G	A	missense_variant c.59C>T p.Thr20Met	yaaA	peroxide stress resistance protein YaaA
317737	snp	T	C	missense_variant c.583A>G p.Thr195Ala	rclC	reactive chlorine species resistance protein C
318076	snp	T	A	missense_variant c.244A>T p.Thr82Ser	rclC	reactive chlorine species resistance protein C
318301	snp	G	T	missense_variant c.19C>A p.Leu7Met	rclC	reactive chlorine species resistance protein C
1007587	snp	A	G	missense_variant c.14T>C p.Ile5Thr	ycbX	6-N-hydroxylaminopurine resistance protein
1007596	snp	G	A	missense_variant c.5C>T p.Ala2Val	ycbX	6-N-hydroxylaminopurine resistance protein
1620120	snp	C	A	missense_variant c.132C>A p.His44Gln	marB	multiple antibiotic resistance protein
2227335	snp	C	A	missense_variant c.1424G>T p.Gly475Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227368	snp	G	A	missense_variant c.1391C>T p.Pro464Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227545	snp	C	A	missense_variant c.1214G>T p.Trp405Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228331	snp	A	T	missense_variant c.428T>A p.Val143Glu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228349	snp	G	A	missense_variant c.410C>T p.Ala137Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228433	snp	C	A	missense_variant c.326G>T p.Arg109Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228463	snp	G	A	missense_variant c.296C>T p.Pro99Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2630599	snp	T	A	missense_variant c.274T>A p.Ser92Thr	yfgI	nalidixic acid resistance protein YfgI
2630850	snp	C	A	missense_variant c.525C>A p.Asp175Glu	yfgI	nalidixic acid resistance protein YfgI
3869486	snp	G	A	missense_variant c.110G>A p.Cys37Tyr	cbrA	colicin M resistance protein
3869713	snp	G	A	missense_variant c.337G>A p.Ala113Thr	cbrA	colicin M resistance protein
3870106	snp	A	G	missense_variant c.730A>G p.Thr244Ala	cbrA	colicin M resistance protein
3870253	snp	A	G	missense_variant c.877A>G p.Thr293Ala	cbrA	colicin M resistance protein
3870268	snp	T	G	missense_variant c.892T>G p.Ser298Ala	cbrA	colicin M resistance protein
3870412	snp	G	A	missense_variant c.1036G>A p.Val346Met	cbrA	colicin M resistance protein
4103027	snp	C	T	missense_variant c.206C>T p.Ala69Val	yiiM	2-amino-6-N-hydroxylaminopurine resistance protein
4103116	snp	T	C	missense_variant c.295T>C p.Tyr99His	yiiM	2-amino-6-N-hydroxylaminopurine resistance protein

ID141

## Error in read.table("ID141_amr_snps", header = T, sep = "\t", dec = ".", : no lines available in input

GenomePosition	Type	ReferenceAllele	AlternateAllele	Consequence	AffectedGene	Product
6239	snp	G	T	missense_variant c.221C>A p.Ala74Glu	yaaA	peroxide stress resistance protein YaaA
6401	snp	G	A	missense_variant c.59C>T p.Thr20Met	yaaA	peroxide stress resistance protein YaaA
317737	snp	T	C	missense_variant c.583A>G p.Thr195Ala	rclC	reactive chlorine species resistance protein C
318076	snp	T	A	missense_variant c.244A>T p.Thr82Ser	rclC	reactive chlorine species resistance protein C
318301	snp	G	T	missense_variant c.19C>A p.Leu7Met	rclC	reactive chlorine species resistance protein C
1007587	snp	A	G	missense_variant c.14T>C p.Ile5Thr	ycbX	6-N-hydroxylaminopurine resistance protein
1007596	snp	G	A	missense_variant c.5C>T p.Ala2Val	ycbX	6-N-hydroxylaminopurine resistance protein
1620120	snp	C	A	missense_variant c.132C>A p.His44Gln	marB	multiple antibiotic resistance protein
2227335	snp	C	A	missense_variant c.1424G>T p.Gly475Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227368	snp	G	A	missense_variant c.1391C>T p.Pro464Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227545	snp	C	A	missense_variant c.1214G>T p.Trp405Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228331	snp	A	T	missense_variant c.428T>A p.Val143Glu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228349	snp	G	A	missense_variant c.410C>T p.Ala137Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228433	snp	C	A	missense_variant c.326G>T p.Arg109Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228463	snp	G	A	missense_variant c.296C>T p.Pro99Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2630599	snp	T	A	missense_variant c.274T>A p.Ser92Thr	yfgI	nalidixic acid resistance protein YfgI
2630850	snp	C	A	missense_variant c.525C>A p.Asp175Glu	yfgI	nalidixic acid resistance protein YfgI
3869486	snp	G	A	missense_variant c.110G>A p.Cys37Tyr	cbrA	colicin M resistance protein
3869713	snp	G	A	missense_variant c.337G>A p.Ala113Thr	cbrA	colicin M resistance protein
3870106	snp	A	G	missense_variant c.730A>G p.Thr244Ala	cbrA	colicin M resistance protein
3870253	snp	A	G	missense_variant c.877A>G p.Thr293Ala	cbrA	colicin M resistance protein
3870268	snp	T	G	missense_variant c.892T>G p.Ser298Ala	cbrA	colicin M resistance protein
3870412	snp	G	A	missense_variant c.1036G>A p.Val346Met	cbrA	colicin M resistance protein
4103027	snp	C	T	missense_variant c.206C>T p.Ala69Val	yiiM	2-amino-6-N-hydroxylaminopurine resistance protein
4103116	snp	T	C	missense_variant c.295T>C p.Tyr99His	yiiM	2-amino-6-N-hydroxylaminopurine resistance protein

ID142

## Error in read.table("ID142_amr_snps", header = T, sep = "\t", dec = ".", : no lines available in input

GenomePosition	Type	ReferenceAllele	AlternateAllele	Consequence	AffectedGene	Product
6239	snp	G	T	missense_variant c.221C>A p.Ala74Glu	yaaA	peroxide stress resistance protein YaaA
6401	snp	G	A	missense_variant c.59C>T p.Thr20Met	yaaA	peroxide stress resistance protein YaaA
317737	snp	T	C	missense_variant c.583A>G p.Thr195Ala	rclC	reactive chlorine species resistance protein C
318076	snp	T	A	missense_variant c.244A>T p.Thr82Ser	rclC	reactive chlorine species resistance protein C
318301	snp	G	T	missense_variant c.19C>A p.Leu7Met	rclC	reactive chlorine species resistance protein C
1007587	snp	A	G	missense_variant c.14T>C p.Ile5Thr	ycbX	6-N-hydroxylaminopurine resistance protein
1007596	snp	G	A	missense_variant c.5C>T p.Ala2Val	ycbX	6-N-hydroxylaminopurine resistance protein
1620120	snp	C	A	missense_variant c.132C>A p.His44Gln	marB	multiple antibiotic resistance protein
2227335	snp	C	A	missense_variant c.1424G>T p.Gly475Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227368	snp	G	A	missense_variant c.1391C>T p.Pro464Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227545	snp	C	A	missense_variant c.1214G>T p.Trp405Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228331	snp	A	T	missense_variant c.428T>A p.Val143Glu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228349	snp	G	A	missense_variant c.410C>T p.Ala137Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228433	snp	C	A	missense_variant c.326G>T p.Arg109Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228463	snp	G	A	missense_variant c.296C>T p.Pro99Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2630599	snp	T	A	missense_variant c.274T>A p.Ser92Thr	yfgI	nalidixic acid resistance protein YfgI
2630850	snp	C	A	missense_variant c.525C>A p.Asp175Glu	yfgI	nalidixic acid resistance protein YfgI
3869486	snp	G	A	missense_variant c.110G>A p.Cys37Tyr	cbrA	colicin M resistance protein
3869713	snp	G	A	missense_variant c.337G>A p.Ala113Thr	cbrA	colicin M resistance protein
3870106	snp	A	G	missense_variant c.730A>G p.Thr244Ala	cbrA	colicin M resistance protein
3870253	snp	A	G	missense_variant c.877A>G p.Thr293Ala	cbrA	colicin M resistance protein
3870268	snp	T	G	missense_variant c.892T>G p.Ser298Ala	cbrA	colicin M resistance protein
3870412	snp	G	A	missense_variant c.1036G>A p.Val346Met	cbrA	colicin M resistance protein
4103027	snp	C	T	missense_variant c.206C>T p.Ala69Val	yiiM	2-amino-6-N-hydroxylaminopurine resistance protein
4103116	snp	T	C	missense_variant c.295T>C p.Tyr99His	yiiM	2-amino-6-N-hydroxylaminopurine resistance protein

ID164

GenomePosition	Type	ReferenceAllele	AlternateAllele	Consequence	AffectedGene	Product
5732	snp	T	G	missense_variant c.728A>C p.Asp243Ala	yaaA	peroxide stress resistance protein YaaA
6162	snp	C	T	missense_variant c.298G>A p.Asp100Asn	yaaA	peroxide stress resistance protein YaaA
6239	snp	G	T	missense_variant c.221C>A p.Ala74Glu	yaaA	peroxide stress resistance protein YaaA
6288	snp	C	T	missense_variant c.172G>A p.Gly58Ser	yaaA	peroxide stress resistance protein YaaA
1007266	snp	C	T	missense_variant c.335G>A p.Gly112Glu	ycbX	6-N-hydroxylaminopurine resistance protein
1500893	snp	C	G	missense_variant c.321C>G p.Cys107Trp	tehA	tellurite resistance protein
2227335	snp	C	A	missense_variant c.1424G>T p.Gly475Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2630545	snp	G	A	missense_variant c.220G>A p.Ala74Thr	yfgI	nalidixic acid resistance protein YfgI
2630629	snp	G	C	missense_variant c.304G>C p.Glu102Gln	yfgI	nalidixic acid resistance protein YfgI

ID169

GenomePosition	Type	ReferenceAllele	AlternateAllele	Consequence	AffectedGene	Product
5732	snp	T	G	missense_variant c.728A>C p.Asp243Ala	yaaA	peroxide stress resistance protein YaaA
317780	snp	T	A	missense_variant c.540A>T p.Glu180Asp	rclC	reactive chlorine species resistance protein C
318312	snp	T	C	missense_variant c.8A>G p.Lys3Arg	rclC	reactive chlorine species resistance protein C
742927	snp	C	T	missense_variant c.101C>T p.Thr34Met	ybgI	radiation resistance protein YbgI
1006777	snp	G	C	missense_variant c.824C>G p.Ala275Gly	ycbX	6-N-hydroxylaminopurine resistance protein
1006933	snp	C	T	missense_variant c.668G>A p.Gly223Asp	ycbX	6-N-hydroxylaminopurine resistance protein
1007042	snp	G	T	missense_variant c.559C>A p.Arg187Ser	ycbX	6-N-hydroxylaminopurine resistance protein
1007131	snp	T	G	missense_variant c.470A>C p.Asp157Ala	ycbX	6-N-hydroxylaminopurine resistance protein
1007587	snp	A	G	missense_variant c.14T>C p.Ile5Thr	ycbX	6-N-hydroxylaminopurine resistance protein
1216402	snp	A	T	missense_variant c.34A>T p.Thr12Ser	ariR	regulator of acid resistance, influenced by indole
1216417	snp	G	T	missense_variant c.49G>T p.Ala17Ser	ariR	regulator of acid resistance, influenced by indole
1441685	snp	T	C	missense_variant c.59A>G p.Asn20Ser	hslJ	lipoprotein implicated in Novobiocin resistance
1441725	snp	A	G	missense_variant c.19T>C p.Phe7Leu	hslJ	lipoprotein implicated in Novobiocin resistance
1500741	snp	A	G	missense_variant c.169A>G p.Ser57Gly	tehA	tellurite resistance protein
1500753	snp	G	A	missense_variant c.181G>A p.Ala61Thr	tehA	tellurite resistance protein
1501299	snp	C	T	missense_variant c.727C>T p.Arg243Cys	tehA	tellurite resistance protein
1620002	snp	C	T	missense_variant c.14C>T p.Ser5Leu	marB	multiple antibiotic resistance protein
1620016	snp	G	A	missense_variant c.28G>A p.Ala10Thr	marB	multiple antibiotic resistance protein
1620086	snp	C	G	missense_variant c.98C>G p.Ala33Gly	marB	multiple antibiotic resistance protein
1620120	snp	C	A	missense_variant c.132C>A p.His44Gln	marB	multiple antibiotic resistance protein
2227335	snp	C	A	missense_variant c.1424G>T p.Gly475Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227452	snp	A	C	missense_variant c.1307T>G p.Leu436Arg	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227653	snp	A	G	missense_variant c.1106T>C p.Ile369Thr	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227818	snp	G	A	missense_variant c.941C>T p.Pro314Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227908	snp	G	A	missense_variant c.851C>T p.Ala284Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227935	snp	T	A	missense_variant c.824A>T p.Asn275Ile	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227949	snp	A	C	missense_variant c.810T>G p.Ser270Arg	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228109	snp	C	G	missense_variant c.650G>C p.Arg217Pro	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228145	snp	C	T	missense_variant c.614G>A p.Cys205Tyr	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228151	snp	C	A	missense_variant c.608G>T p.Arg203Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228241	snp	C	T	missense_variant c.518G>A p.Gly173Glu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228265	snp	G	A	missense_variant c.494C>T p.Pro165Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228277	snp	C	T	missense_variant c.482G>A p.Arg161Gln	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228349	snp	G	A	missense_variant c.410C>T p.Ala137Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228367	snp	C	A	missense_variant c.392G>T p.Arg131Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228397	snp	G	C	missense_variant c.362C>G p.Ala121Gly	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228406	snp	C	A	missense_variant c.353G>T p.Arg118Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228433	snp	C	A	missense_variant c.326G>T p.Arg109Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228463	snp	G	A	missense_variant c.296C>T p.Pro99Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2630395	snp	G	A	missense_variant c.70G>A p.Asp24Asn	yfgI	nalidixic acid resistance protein YfgI
2630599	snp	T	A	missense_variant c.274T>A p.Ser92Thr	yfgI	nalidixic acid resistance protein YfgI
3869965	snp	T	G	missense_variant c.589T>G p.Ser197Ala	cbrA	colicin M resistance protein
3869974	snp	A	G	missense_variant c.598A>G p.Asn200Asp	cbrA	colicin M resistance protein
3870106	snp	A	G	missense_variant c.730A>G p.Thr244Ala	cbrA	colicin M resistance protein
3870253	snp	A	G	missense_variant c.877A>G p.Thr293Ala	cbrA	colicin M resistance protein
3870258	snp	C	G	missense_variant c.882C>G p.Asp294Glu	cbrA	colicin M resistance protein
4102929	snp	G	C	missense_variant c.108G>C p.Glu36Asp	yiiM	2-amino-6-N-hydroxylaminopurine resistance protein

ID177

GenomePosition	Type	ReferenceAllele	AlternateAllele	Consequence	AffectedGene	Product
5732	snp	T	G	missense_variant c.728A>C p.Asp243Ala	yaaA	peroxide stress resistance protein YaaA
6239	snp	G	T	missense_variant c.221C>A p.Ala74Glu	yaaA	peroxide stress resistance protein YaaA
318076	snp	T	A	missense_variant c.244A>T p.Thr82Ser	rclC	reactive chlorine species resistance protein C
743181	snp	A	T	missense_variant c.355A>T p.Thr119Ser	ybgI	radiation resistance protein YbgI
1007522	snp	C	T	missense_variant c.79G>A p.Val27Ile	ycbX	6-N-hydroxylaminopurine resistance protein
1007576	snp	T	C	missense_variant c.25A>G p.Ile9Val	ycbX	6-N-hydroxylaminopurine resistance protein
1007587	snp	A	G	missense_variant c.14T>C p.Ile5Thr	ycbX	6-N-hydroxylaminopurine resistance protein
1216417	snp	G	T	missense_variant c.49G>T p.Ala17Ser	ariR	regulator of acid resistance, influenced by indole
1441506	snp	C	T	missense_variant c.238G>A p.Glu80Lys	hslJ	lipoprotein implicated in Novobiocin resistance
1500753	snp	G	A	missense_variant c.181G>A p.Ala61Thr	tehA	tellurite resistance protein
1620002	snp	C	T	missense_variant c.14C>T p.Ser5Leu	marB	multiple antibiotic resistance protein
1620022	snp	C	T	missense_variant c.34C>T p.Leu12Phe	marB	multiple antibiotic resistance protein
1620037	snp	G	A	missense_variant c.49G>A p.Ala17Thr	marB	multiple antibiotic resistance protein
1620046	snp	G	A	missense_variant c.58G>A p.Val20Ile	marB	multiple antibiotic resistance protein
1620120	snp	C	A	missense_variant c.132C>A p.His44Gln	marB	multiple antibiotic resistance protein
2227326	snp	G	A	missense_variant c.1433C>T p.Ala478Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227335	snp	C	A	missense_variant c.1424G>T p.Gly475Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227368	snp	G	A	missense_variant c.1391C>T p.Pro464Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227422	snp	G	C	missense_variant c.1337C>G p.Pro446Arg	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227443	snp	G	C	missense_variant c.1316C>G p.Ala439Gly	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227452	snp	A	C	missense_variant c.1307T>G p.Leu436Arg	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227563	snp	G	A	missense_variant c.1196C>T p.Pro399Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227653	snp	A	G	missense_variant c.1106T>C p.Ile369Thr	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227668	snp	A	G	missense_variant c.1091T>C p.Val364Ala	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227818	snp	G	A	missense_variant c.941C>T p.Pro314Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227935	snp	T	A	missense_variant c.824A>T p.Asn275Ile	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227949	snp	A	C	missense_variant c.810T>G p.Ser270Arg	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228109	snp	C	G	missense_variant c.650G>C p.Arg217Pro	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228145	snp	C	T	missense_variant c.614G>A p.Cys205Tyr	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228151	snp	C	A	missense_variant c.608G>T p.Arg203Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228190	snp	G	A	missense_variant c.569C>T p.Ala190Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228265	snp	G	A	missense_variant c.494C>T p.Pro165Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228349	snp	G	A	missense_variant c.410C>T p.Ala137Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228397	snp	G	C	missense_variant c.362C>G p.Ala121Gly	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228433	snp	C	A	missense_variant c.326G>T p.Arg109Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228444	snp	T	G	missense_variant c.315A>C p.Arg105Ser	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228502	snp	C	T	missense_variant c.257G>A p.Ser86Asn	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228553	snp	G	T	missense_variant c.206C>A p.Pro69His	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2630356	snp	G	A	missense_variant c.31G>A p.Ala11Thr	yfgI	nalidixic acid resistance protein YfgI
2630599	snp	T	A	missense_variant c.274T>A p.Ser92Thr	yfgI	nalidixic acid resistance protein YfgI
3635277	snp	C	T	missense_variant c.437C>T p.Thr146Ile	yhiM	inner membrane protein with a role in acid resistance
3635534	snp	T	A	missense_variant c.694T>A p.Phe232Ile	yhiM	inner membrane protein with a role in acid resistance
3869635	snp	C	T	missense_variant c.259C>T p.Leu87Phe	cbrA	colicin M resistance protein
3869965	snp	T	G	missense_variant c.589T>G p.Ser197Ala	cbrA	colicin M resistance protein
3869974	snp	A	G	missense_variant c.598A>G p.Asn200Asp	cbrA	colicin M resistance protein
3870080	snp	G	A	missense_variant c.704G>A p.Ser235Asn	cbrA	colicin M resistance protein
3870253	snp	A	G	missense_variant c.877A>G p.Thr293Ala	cbrA	colicin M resistance protein
3870258	snp	C	G	missense_variant c.882C>G p.Asp294Glu	cbrA	colicin M resistance protein
4103121	snp	G	T	missense_variant c.300G>T p.Met100Ile	yiiM	2-amino-6-N-hydroxylaminopurine resistance protein

ID178

GenomePosition	Type	ReferenceAllele	AlternateAllele	Consequence	AffectedGene	Product
5732	snp	T	G	missense_variant c.728A>C p.Asp243Ala	yaaA	peroxide stress resistance protein YaaA
6408	snp	T	G	missense_variant c.52A>C p.Thr18Pro	yaaA	peroxide stress resistance protein YaaA
317780	snp	T	A	missense_variant c.540A>T p.Glu180Asp	rclC	reactive chlorine species resistance protein C
318076	snp	T	A	missense_variant c.244A>T p.Thr82Ser	rclC	reactive chlorine species resistance protein C
1007042	snp	G	T	missense_variant c.559C>A p.Arg187Ser	ycbX	6-N-hydroxylaminopurine resistance protein
1007428	snp	G	A	missense_variant c.173C>T p.Thr58Ile	ycbX	6-N-hydroxylaminopurine resistance protein
1007587	snp	A	G	missense_variant c.14T>C p.Ile5Thr	ycbX	6-N-hydroxylaminopurine resistance protein
1216402	snp	A	G	missense_variant c.34A>G p.Thr12Ala	ariR	regulator of acid resistance, influenced by indole
1216417	snp	G	T	missense_variant c.49G>T p.Ala17Ser	ariR	regulator of acid resistance, influenced by indole
1216562	snp	G	A	missense_variant c.194G>A p.Ser65Asn	ariR	regulator of acid resistance, influenced by indole
1500615	snp	G	A	missense_variant c.43G>A p.Gly15Ser	tehA	tellurite resistance protein
1500741	snp	A	G	missense_variant c.169A>G p.Ser57Gly	tehA	tellurite resistance protein
1500753	snp	G	A	missense_variant c.181G>A p.Ala61Thr	tehA	tellurite resistance protein
1501399	snp	G	T	missense_variant c.827G>T p.Ser276Ile	tehA	tellurite resistance protein
1501518	snp	G	A	missense_variant c.946G>A p.Val316Ile	tehA	tellurite resistance protein
1620002	snp	C	T	missense_variant c.14C>T p.Ser5Leu	marB	multiple antibiotic resistance protein
1620120	snp	C	A	missense_variant c.132C>A p.His44Gln	marB	multiple antibiotic resistance protein
2227335	snp	C	A	missense_variant c.1424G>T p.Gly475Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227353	snp	A	G	missense_variant c.1406T>C p.Leu469Pro	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227510	snp	C	T	missense_variant c.1249G>A p.Ala417Thr	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227560	snp	A	G	missense_variant c.1199T>C p.Val400Ala	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227566	snp	T	C	missense_variant c.1193A>G p.Gln398Arg	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227653	snp	A	G	missense_variant c.1106T>C p.Ile369Thr	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227872	snp	G	C	missense_variant c.887C>G p.Pro296Arg	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227935	snp	T	A	missense_variant c.824A>T p.Asn275Ile	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227949	snp	A	C	missense_variant c.810T>G p.Ser270Arg	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228109	snp	C	G	missense_variant c.650G>C p.Arg217Pro	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228239	snp	G	A	missense_variant c.520C>T p.Arg174Trp	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228265	snp	G	A	missense_variant c.494C>T p.Pro165Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228349	snp	G	A	missense_variant c.410C>T p.Ala137Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228367	snp	C	A	missense_variant c.392G>T p.Arg131Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228397	snp	G	C	missense_variant c.362C>G p.Ala121Gly	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228433	snp	C	A	missense_variant c.326G>T p.Arg109Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2630364	snp	A	T	missense_variant c.39A>T p.Leu13Phe	yfgI	nalidixic acid resistance protein YfgI
2630599	snp	T	A	missense_variant c.274T>A p.Ser92Thr	yfgI	nalidixic acid resistance protein YfgI
3635534	snp	T	A	missense_variant c.694T>A p.Phe232Ile	yhiM	inner membrane protein with a role in acid resistance
3635595	snp	C	T	missense_variant c.755C>T p.Ala252Val	yhiM	inner membrane protein with a role in acid resistance
3869965	snp	T	G	missense_variant c.589T>G p.Ser197Ala	cbrA	colicin M resistance protein
3869974	snp	A	G	missense_variant c.598A>G p.Asn200Asp	cbrA	colicin M resistance protein
3870080	snp	G	A	missense_variant c.704G>A p.Ser235Asn	cbrA	colicin M resistance protein
3870253	snp	A	G	missense_variant c.877A>G p.Thr293Ala	cbrA	colicin M resistance protein
3870258	snp	C	G	missense_variant c.882C>G p.Asp294Glu	cbrA	colicin M resistance protein
3870295	snp	C	A	missense_variant c.919C>A p.Leu307Ile	cbrA	colicin M resistance protein
4102964	snp	A	T	missense_variant c.143A>T p.Lys48Met	yiiM	2-amino-6-N-hydroxylaminopurine resistance protein

ID182

GenomePosition	Type	ReferenceAllele	AlternateAllele	Consequence	AffectedGene	Product
5732	snp	T	G	missense_variant c.728A>C p.Asp243Ala	yaaA	peroxide stress resistance protein YaaA
6239	snp	G	T	missense_variant c.221C>A p.Ala74Glu	yaaA	peroxide stress resistance protein YaaA
742927	snp	C	A	missense_variant c.101C>A p.Thr34Lys	ybgI	radiation resistance protein YbgI
1007042	snp	G	T	missense_variant c.559C>A p.Arg187Ser	ycbX	6-N-hydroxylaminopurine resistance protein
1007111	snp	C	T	missense_variant c.490G>A p.Ala164Thr	ycbX	6-N-hydroxylaminopurine resistance protein
1007587	snp	A	G	missense_variant c.14T>C p.Ile5Thr	ycbX	6-N-hydroxylaminopurine resistance protein
1500753	snp	G	A	missense_variant c.181G>A p.Ala61Thr	tehA	tellurite resistance protein
1620120	snp	C	A	missense_variant c.132C>A p.His44Gln	marB	multiple antibiotic resistance protein
2227335	snp	C	A	missense_variant c.1424G>T p.Gly475Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228553	snp	G	T	missense_variant c.206C>A p.Pro69His	mdtQ	putative multidrug resistance outer membrane protein MdtQ
3869407	snp	C	A	missense_variant c.31C>A p.Leu11Ile	cbrA	colicin M resistance protein
3869713	snp	G	A	missense_variant c.337G>A p.Ala113Thr	cbrA	colicin M resistance protein
3870106	snp	A	G	missense_variant c.730A>G p.Thr244Ala	cbrA	colicin M resistance protein
3870253	snp	A	G	missense_variant c.877A>G p.Thr293Ala	cbrA	colicin M resistance protein
3870268	snp	T	G	missense_variant c.892T>G p.Ser298Ala	cbrA	colicin M resistance protein
3870412	snp	G	A	missense_variant c.1036G>A p.Val346Met	cbrA	colicin M resistance protein

ID186

GenomePosition	Type	ReferenceAllele	AlternateAllele	Consequence	AffectedGene	Product
6239	snp	G	T	missense_variant c.221C>A p.Ala74Glu	yaaA	peroxide stress resistance protein YaaA
6401	snp	G	A	missense_variant c.59C>T p.Thr20Met	yaaA	peroxide stress resistance protein YaaA
317737	snp	T	C	missense_variant c.583A>G p.Thr195Ala	rclC	reactive chlorine species resistance protein C
318076	snp	T	A	missense_variant c.244A>T p.Thr82Ser	rclC	reactive chlorine species resistance protein C
318301	snp	G	T	missense_variant c.19C>A p.Leu7Met	rclC	reactive chlorine species resistance protein C
1007587	snp	A	G	missense_variant c.14T>C p.Ile5Thr	ycbX	6-N-hydroxylaminopurine resistance protein
1007596	snp	G	A	missense_variant c.5C>T p.Ala2Val	ycbX	6-N-hydroxylaminopurine resistance protein
1620120	snp	C	A	missense_variant c.132C>A p.His44Gln	marB	multiple antibiotic resistance protein
2227335	snp	C	A	missense_variant c.1424G>T p.Gly475Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227368	snp	G	A	missense_variant c.1391C>T p.Pro464Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227545	snp	C	A	missense_variant c.1214G>T p.Trp405Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228331	snp	A	T	missense_variant c.428T>A p.Val143Glu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228349	snp	G	A	missense_variant c.410C>T p.Ala137Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228433	snp	C	A	missense_variant c.326G>T p.Arg109Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228463	snp	G	A	missense_variant c.296C>T p.Pro99Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
3869713	snp	G	A	missense_variant c.337G>A p.Ala113Thr	cbrA	colicin M resistance protein
3869965	snp	T	G	missense_variant c.589T>G p.Ser197Ala	cbrA	colicin M resistance protein
3869974	snp	A	G	missense_variant c.598A>G p.Asn200Asp	cbrA	colicin M resistance protein
3870106	snp	A	G	missense_variant c.730A>G p.Thr244Ala	cbrA	colicin M resistance protein
3870253	snp	A	G	missense_variant c.877A>G p.Thr293Ala	cbrA	colicin M resistance protein
3870412	snp	G	A	missense_variant c.1036G>A p.Val346Met	cbrA	colicin M resistance protein
4103027	snp	C	T	missense_variant c.206C>T p.Ala69Val	yiiM	2-amino-6-N-hydroxylaminopurine resistance protein
4103116	snp	T	C	missense_variant c.295T>C p.Tyr99His	yiiM	2-amino-6-N-hydroxylaminopurine resistance protein

ID187

GenomePosition	Type	ReferenceAllele	AlternateAllele	Consequence	AffectedGene	Product
1006759	snp	G	A	missense_variant c.842C>T p.Ala281Val	ycbX	6-N-hydroxylaminopurine resistance protein
1007042	snp	G	T	missense_variant c.559C>A p.Arg187Ser	ycbX	6-N-hydroxylaminopurine resistance protein
1007587	snp	A	G	missense_variant c.14T>C p.Ile5Thr	ycbX	6-N-hydroxylaminopurine resistance protein
1441685	snp	T	C	missense_variant c.59A>G p.Asn20Ser	hslJ	lipoprotein implicated in Novobiocin resistance
1441725	snp	A	G	missense_variant c.19T>C p.Phe7Leu	hslJ	lipoprotein implicated in Novobiocin resistance
1501490	snp	T	G	missense_variant c.918T>G p.Phe306Leu	tehA	tellurite resistance protein
1620002	snp	C	T	missense_variant c.14C>T p.Ser5Leu	marB	multiple antibiotic resistance protein
1620031	snp	T	A	missense_variant c.43T>A p.Phe15Ile	marB	multiple antibiotic resistance protein
1620120	snp	C	A	missense_variant c.132C>A p.His44Gln	marB	multiple antibiotic resistance protein
2227335	snp	C	A	missense_variant c.1424G>T p.Gly475Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227587	snp	C	T	missense_variant c.1172G>A p.Arg391Gln	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227653	snp	A	G	missense_variant c.1106T>C p.Ile369Thr	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227872	snp	G	C	missense_variant c.887C>G p.Pro296Arg	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227953	snp	T	A	missense_variant c.806A>T p.Gln269Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227968	snp	A	G	missense_variant c.791T>C p.Leu264Ser	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228553	snp	G	T	missense_variant c.206C>A p.Pro69His	mdtQ	putative multidrug resistance outer membrane protein MdtQ
3869383	snp	C	T	missense_variant c.7C>T p.His3Tyr	cbrA	colicin M resistance protein
3869407	snp	C	A	missense_variant c.31C>A p.Leu11Ile	cbrA	colicin M resistance protein
3869713	snp	G	A	missense_variant c.337G>A p.Ala113Thr	cbrA	colicin M resistance protein
3870106	snp	A	G	missense_variant c.730A>G p.Thr244Ala	cbrA	colicin M resistance protein
3870253	snp	A	G	missense_variant c.877A>G p.Thr293Ala	cbrA	colicin M resistance protein
3870268	snp	T	G	missense_variant c.892T>G p.Ser298Ala	cbrA	colicin M resistance protein
3870412	snp	G	A	missense_variant c.1036G>A p.Val346Met	cbrA	colicin M resistance protein

ID195

GenomePosition	Type	ReferenceAllele	AlternateAllele	Consequence	AffectedGene	Product
6239	snp	G	T	missense_variant c.221C>A p.Ala74Glu	yaaA	peroxide stress resistance protein YaaA
1007042	snp	G	T	missense_variant c.559C>A p.Arg187Ser	ycbX	6-N-hydroxylaminopurine resistance protein
1007587	snp	A	G	missense_variant c.14T>C p.Ile5Thr	ycbX	6-N-hydroxylaminopurine resistance protein
1441604	snp	C	T	missense_variant c.140G>A p.Ser47Asn	hslJ	lipoprotein implicated in Novobiocin resistance
1500753	snp	G	A	missense_variant c.181G>A p.Ala61Thr	tehA	tellurite resistance protein
1620120	snp	C	A	missense_variant c.132C>A p.His44Gln	marB	multiple antibiotic resistance protein
2227335	snp	C	A	missense_variant c.1424G>T p.Gly475Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227368	snp	G	A	missense_variant c.1391C>T p.Pro464Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227545	snp	C	A	missense_variant c.1214G>T p.Trp405Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228331	snp	A	T	missense_variant c.428T>A p.Val143Glu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228349	snp	G	A	missense_variant c.410C>T p.Ala137Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228433	snp	C	A	missense_variant c.326G>T p.Arg109Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228463	snp	G	A	missense_variant c.296C>T p.Pro99Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228556	snp	A	C	missense_variant c.203T>G p.Leu68Arg	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2630599	snp	T	A	missense_variant c.274T>A p.Ser92Thr	yfgI	nalidixic acid resistance protein YfgI
2630850	snp	C	A	missense_variant c.525C>A p.Asp175Glu	yfgI	nalidixic acid resistance protein YfgI
3870106	snp	A	G	missense_variant c.730A>G p.Thr244Ala	cbrA	colicin M resistance protein
3870253	snp	A	G	missense_variant c.877A>G p.Thr293Ala	cbrA	colicin M resistance protein
3870412	snp	G	A	missense_variant c.1036G>A p.Val346Met	cbrA	colicin M resistance protein

ID197

GenomePosition	Type	ReferenceAllele	AlternateAllele	Consequence	AffectedGene	Product
5732	snp	T	G	missense_variant c.728A>C p.Asp243Ala	yaaA	peroxide stress resistance protein YaaA
6162	snp	C	T	missense_variant c.298G>A p.Asp100Asn	yaaA	peroxide stress resistance protein YaaA
6239	snp	G	T	missense_variant c.221C>A p.Ala74Glu	yaaA	peroxide stress resistance protein YaaA
6288	snp	C	T	missense_variant c.172G>A p.Gly58Ser	yaaA	peroxide stress resistance protein YaaA
1007266	snp	C	T	missense_variant c.335G>A p.Gly112Glu	ycbX	6-N-hydroxylaminopurine resistance protein
1500893	snp	C	G	missense_variant c.321C>G p.Cys107Trp	tehA	tellurite resistance protein
2227335	snp	C	A	missense_variant c.1424G>T p.Gly475Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228304	snp	A	C	missense_variant c.455T>G p.Ile152Ser	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2630545	snp	G	A	missense_variant c.220G>A p.Ala74Thr	yfgI	nalidixic acid resistance protein YfgI
2630629	snp	G	C	missense_variant c.304G>C p.Glu102Gln	yfgI	nalidixic acid resistance protein YfgI

ID199

GenomePosition	Type	ReferenceAllele	AlternateAllele	Consequence	AffectedGene	Product
6239	snp	G	T	missense_variant c.221C>A p.Ala74Glu	yaaA	peroxide stress resistance protein YaaA
6339	snp	G	T	missense_variant c.121C>A p.Leu41Met	yaaA	peroxide stress resistance protein YaaA
318076	snp	T	A	missense_variant c.244A>T p.Thr82Ser	rclC	reactive chlorine species resistance protein C
1007042	snp	G	T	missense_variant c.559C>A p.Arg187Ser	ycbX	6-N-hydroxylaminopurine resistance protein
1007270	snp	T	G	missense_variant c.331A>C p.Ser111Arg	ycbX	6-N-hydroxylaminopurine resistance protein
1007587	snp	A	G	missense_variant c.14T>C p.Ile5Thr	ycbX	6-N-hydroxylaminopurine resistance protein
1007596	snp	G	A	missense_variant c.5C>T p.Ala2Val	ycbX	6-N-hydroxylaminopurine resistance protein
1169131	snp	G	A	missense_variant c.59G>A p.Ser20Asn	bhsA	DUF1471 domain-containing multiple stress resistance outer membrane protein BhsA
1441734	snp	C	G	missense_variant c.10G>C p.Val4Leu	hslJ	lipoprotein implicated in Novobiocin resistance
1500753	snp	G	A	missense_variant c.181G>A p.Ala61Thr	tehA	tellurite resistance protein
1500807	snp	C	A	missense_variant c.235C>A p.Leu79Met	tehA	tellurite resistance protein
1501409	snp	T	A	missense_variant c.837T>A p.Asp279Glu	tehA	tellurite resistance protein
1620002	snp	C	T	missense_variant c.14C>T p.Ser5Leu	marB	multiple antibiotic resistance protein
1620037	snp	G	A	missense_variant c.49G>A p.Ala17Thr	marB	multiple antibiotic resistance protein
1620046	snp	G	A	missense_variant c.58G>A p.Val20Ile	marB	multiple antibiotic resistance protein
1620120	snp	C	A	missense_variant c.132C>A p.His44Gln	marB	multiple antibiotic resistance protein
2227335	snp	C	A	missense_variant c.1424G>T p.Gly475Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227368	snp	G	A	missense_variant c.1391C>T p.Pro464Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227545	snp	C	A	missense_variant c.1214G>T p.Trp405Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228032	snp	G	T	missense_variant c.727C>A p.Pro243Thr	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228331	snp	A	T	missense_variant c.428T>A p.Val143Glu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228349	snp	G	A	missense_variant c.410C>T p.Ala137Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228433	snp	C	A	missense_variant c.326G>T p.Arg109Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228463	snp	G	A	missense_variant c.296C>T p.Pro99Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2630599	snp	T	A	missense_variant c.274T>A p.Ser92Thr	yfgI	nalidixic acid resistance protein YfgI
2630850	snp	C	A	missense_variant c.525C>A p.Asp175Glu	yfgI	nalidixic acid resistance protein YfgI
3870106	snp	A	G	missense_variant c.730A>G p.Thr244Ala	cbrA	colicin M resistance protein
3870253	snp	A	G	missense_variant c.877A>G p.Thr293Ala	cbrA	colicin M resistance protein
3870268	snp	T	G	missense_variant c.892T>G p.Ser298Ala	cbrA	colicin M resistance protein
3870412	snp	G	A	missense_variant c.1036G>A p.Val346Met	cbrA	colicin M resistance protein

ID208

GenomePosition	Type	ReferenceAllele	AlternateAllele	Consequence	AffectedGene	Product
6239	snp	G	T	missense_variant c.221C>A p.Ala74Glu	yaaA	peroxide stress resistance protein YaaA
317780	snp	T	A	missense_variant c.540A>T p.Glu180Asp	rclC	reactive chlorine species resistance protein C
318076	snp	T	A	missense_variant c.244A>T p.Thr82Ser	rclC	reactive chlorine species resistance protein C
1007042	snp	G	T	missense_variant c.559C>A p.Arg187Ser	ycbX	6-N-hydroxylaminopurine resistance protein
1007428	snp	G	A	missense_variant c.173C>T p.Thr58Ile	ycbX	6-N-hydroxylaminopurine resistance protein
1007587	snp	A	G	missense_variant c.14T>C p.Ile5Thr	ycbX	6-N-hydroxylaminopurine resistance protein
1216402	snp	A	G	missense_variant c.34A>G p.Thr12Ala	ariR	regulator of acid resistance, influenced by indole
1216417	snp	G	T	missense_variant c.49G>T p.Ala17Ser	ariR	regulator of acid resistance, influenced by indole
1216562	snp	G	A	missense_variant c.194G>A p.Ser65Asn	ariR	regulator of acid resistance, influenced by indole
1500615	snp	G	A	missense_variant c.43G>A p.Gly15Ser	tehA	tellurite resistance protein
1500741	snp	A	G	missense_variant c.169A>G p.Ser57Gly	tehA	tellurite resistance protein
1500753	snp	G	A	missense_variant c.181G>A p.Ala61Thr	tehA	tellurite resistance protein
1501399	snp	G	T	missense_variant c.827G>T p.Ser276Ile	tehA	tellurite resistance protein
1501518	snp	G	A	missense_variant c.946G>A p.Val316Ile	tehA	tellurite resistance protein
1620002	snp	C	T	missense_variant c.14C>T p.Ser5Leu	marB	multiple antibiotic resistance protein
1620120	snp	C	A	missense_variant c.132C>A p.His44Gln	marB	multiple antibiotic resistance protein
2227335	snp	C	A	missense_variant c.1424G>T p.Gly475Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227353	snp	A	G	missense_variant c.1406T>C p.Leu469Pro	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227510	snp	C	T	missense_variant c.1249G>A p.Ala417Thr	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227560	snp	A	G	missense_variant c.1199T>C p.Val400Ala	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227566	snp	T	C	missense_variant c.1193A>G p.Gln398Arg	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227653	snp	A	G	missense_variant c.1106T>C p.Ile369Thr	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227872	snp	G	C	missense_variant c.887C>G p.Pro296Arg	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227935	snp	T	A	missense_variant c.824A>T p.Asn275Ile	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227949	snp	A	C	missense_variant c.810T>G p.Ser270Arg	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228109	snp	C	G	missense_variant c.650G>C p.Arg217Pro	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228239	snp	G	A	missense_variant c.520C>T p.Arg174Trp	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228265	snp	G	A	missense_variant c.494C>T p.Pro165Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228349	snp	G	A	missense_variant c.410C>T p.Ala137Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228367	snp	C	A	missense_variant c.392G>T p.Arg131Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228397	snp	G	C	missense_variant c.362C>G p.Ala121Gly	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228433	snp	C	A	missense_variant c.326G>T p.Arg109Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2630364	snp	A	T	missense_variant c.39A>T p.Leu13Phe	yfgI	nalidixic acid resistance protein YfgI
2630599	snp	T	A	missense_variant c.274T>A p.Ser92Thr	yfgI	nalidixic acid resistance protein YfgI
3635534	snp	T	A	missense_variant c.694T>A p.Phe232Ile	yhiM	inner membrane protein with a role in acid resistance
3635595	snp	C	T	missense_variant c.755C>T p.Ala252Val	yhiM	inner membrane protein with a role in acid resistance
3869965	snp	T	G	missense_variant c.589T>G p.Ser197Ala	cbrA	colicin M resistance protein
3869974	snp	A	G	missense_variant c.598A>G p.Asn200Asp	cbrA	colicin M resistance protein
3870080	snp	G	A	missense_variant c.704G>A p.Ser235Asn	cbrA	colicin M resistance protein
3870253	snp	A	G	missense_variant c.877A>G p.Thr293Ala	cbrA	colicin M resistance protein
3870258	snp	C	G	missense_variant c.882C>G p.Asp294Glu	cbrA	colicin M resistance protein
3870295	snp	C	A	missense_variant c.919C>A p.Leu307Ile	cbrA	colicin M resistance protein
4102964	snp	A	T	missense_variant c.143A>T p.Lys48Met	yiiM	2-amino-6-N-hydroxylaminopurine resistance protein

ID214

GenomePosition	Type	ReferenceAllele	AlternateAllele	Consequence	AffectedGene	Product
5732	snp	T	G	missense_variant c.728A>C p.Asp243Ala	yaaA	peroxide stress resistance protein YaaA
6162	snp	C	T	missense_variant c.298G>A p.Asp100Asn	yaaA	peroxide stress resistance protein YaaA
6239	snp	G	T	missense_variant c.221C>A p.Ala74Glu	yaaA	peroxide stress resistance protein YaaA
6288	snp	C	T	missense_variant c.172G>A p.Gly58Ser	yaaA	peroxide stress resistance protein YaaA
1007266	snp	C	T	missense_variant c.335G>A p.Gly112Glu	ycbX	6-N-hydroxylaminopurine resistance protein
1500893	snp	C	G	missense_variant c.321C>G p.Cys107Trp	tehA	tellurite resistance protein
2227335	snp	C	A	missense_variant c.1424G>T p.Gly475Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2630545	snp	G	A	missense_variant c.220G>A p.Ala74Thr	yfgI	nalidixic acid resistance protein YfgI
2630629	snp	G	C	missense_variant c.304G>C p.Glu102Gln	yfgI	nalidixic acid resistance protein YfgI
3657346	snp	G	A	missense_variant c.352G>A p.Ala118Thr	hdeD	acid-resistance membrane protein

ID224

GenomePosition	Type	ReferenceAllele	AlternateAllele	Consequence	AffectedGene	Product
5732	snp	T	G	missense_variant c.728A>C p.Asp243Ala	yaaA	peroxide stress resistance protein YaaA
6162	snp	C	T	missense_variant c.298G>A p.Asp100Asn	yaaA	peroxide stress resistance protein YaaA
6239	snp	G	T	missense_variant c.221C>A p.Ala74Glu	yaaA	peroxide stress resistance protein YaaA
1007266	snp	C	T	missense_variant c.335G>A p.Gly112Glu	ycbX	6-N-hydroxylaminopurine resistance protein
2227335	snp	C	A	missense_variant c.1424G>T p.Gly475Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228170	snp	G	A	missense_variant c.589C>T p.Pro197Ser	mdtQ	putative multidrug resistance outer membrane protein MdtQ

ID228

GenomePosition	Type	ReferenceAllele	AlternateAllele	Consequence	AffectedGene	Product
5732	snp	T	G	missense_variant c.728A>C p.Asp243Ala	yaaA	peroxide stress resistance protein YaaA
317780	snp	T	A	missense_variant c.540A>T p.Glu180Asp	rclC	reactive chlorine species resistance protein C
318312	snp	T	C	missense_variant c.8A>G p.Lys3Arg	rclC	reactive chlorine species resistance protein C
742927	snp	C	T	missense_variant c.101C>T p.Thr34Met	ybgI	radiation resistance protein YbgI
1006777	snp	G	C	missense_variant c.824C>G p.Ala275Gly	ycbX	6-N-hydroxylaminopurine resistance protein
1006933	snp	C	T	missense_variant c.668G>A p.Gly223Asp	ycbX	6-N-hydroxylaminopurine resistance protein
1007042	snp	G	T	missense_variant c.559C>A p.Arg187Ser	ycbX	6-N-hydroxylaminopurine resistance protein
1007131	snp	T	G	missense_variant c.470A>C p.Asp157Ala	ycbX	6-N-hydroxylaminopurine resistance protein
1007587	snp	A	G	missense_variant c.14T>C p.Ile5Thr	ycbX	6-N-hydroxylaminopurine resistance protein
1216402	snp	A	T	missense_variant c.34A>T p.Thr12Ser	ariR	regulator of acid resistance, influenced by indole
1216417	snp	G	T	missense_variant c.49G>T p.Ala17Ser	ariR	regulator of acid resistance, influenced by indole
1441685	snp	T	C	missense_variant c.59A>G p.Asn20Ser	hslJ	lipoprotein implicated in Novobiocin resistance
1441725	snp	A	G	missense_variant c.19T>C p.Phe7Leu	hslJ	lipoprotein implicated in Novobiocin resistance
1500741	snp	A	G	missense_variant c.169A>G p.Ser57Gly	tehA	tellurite resistance protein
1500753	snp	G	A	missense_variant c.181G>A p.Ala61Thr	tehA	tellurite resistance protein
1501299	snp	C	T	missense_variant c.727C>T p.Arg243Cys	tehA	tellurite resistance protein
1620002	snp	C	T	missense_variant c.14C>T p.Ser5Leu	marB	multiple antibiotic resistance protein
1620016	snp	G	A	missense_variant c.28G>A p.Ala10Thr	marB	multiple antibiotic resistance protein
1620086	snp	C	G	missense_variant c.98C>G p.Ala33Gly	marB	multiple antibiotic resistance protein
1620120	snp	C	A	missense_variant c.132C>A p.His44Gln	marB	multiple antibiotic resistance protein
2227335	snp	C	A	missense_variant c.1424G>T p.Gly475Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227452	snp	A	C	missense_variant c.1307T>G p.Leu436Arg	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227653	snp	A	G	missense_variant c.1106T>C p.Ile369Thr	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227818	snp	G	A	missense_variant c.941C>T p.Pro314Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227908	snp	G	A	missense_variant c.851C>T p.Ala284Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227935	snp	T	A	missense_variant c.824A>T p.Asn275Ile	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227949	snp	A	C	missense_variant c.810T>G p.Ser270Arg	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228109	snp	C	G	missense_variant c.650G>C p.Arg217Pro	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228145	snp	C	T	missense_variant c.614G>A p.Cys205Tyr	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228151	snp	C	A	missense_variant c.608G>T p.Arg203Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228241	snp	C	T	missense_variant c.518G>A p.Gly173Glu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228265	snp	G	A	missense_variant c.494C>T p.Pro165Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228277	snp	C	T	missense_variant c.482G>A p.Arg161Gln	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228349	snp	G	A	missense_variant c.410C>T p.Ala137Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228367	snp	C	A	missense_variant c.392G>T p.Arg131Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228397	snp	G	C	missense_variant c.362C>G p.Ala121Gly	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228406	snp	C	A	missense_variant c.353G>T p.Arg118Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228433	snp	C	A	missense_variant c.326G>T p.Arg109Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228463	snp	G	A	missense_variant c.296C>T p.Pro99Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2630395	snp	G	A	missense_variant c.70G>A p.Asp24Asn	yfgI	nalidixic acid resistance protein YfgI
2630599	snp	T	A	missense_variant c.274T>A p.Ser92Thr	yfgI	nalidixic acid resistance protein YfgI
3869965	snp	T	G	missense_variant c.589T>G p.Ser197Ala	cbrA	colicin M resistance protein
3869974	snp	A	G	missense_variant c.598A>G p.Asn200Asp	cbrA	colicin M resistance protein
3870106	snp	A	G	missense_variant c.730A>G p.Thr244Ala	cbrA	colicin M resistance protein
3870253	snp	A	G	missense_variant c.877A>G p.Thr293Ala	cbrA	colicin M resistance protein
3870258	snp	C	G	missense_variant c.882C>G p.Asp294Glu	cbrA	colicin M resistance protein
4102929	snp	G	C	missense_variant c.108G>C p.Glu36Asp	yiiM	2-amino-6-N-hydroxylaminopurine resistance protein

ID229

GenomePosition	Type	ReferenceAllele	AlternateAllele	Consequence	AffectedGene	Product
6239	snp	G	T	missense_variant c.221C>A p.Ala74Glu	yaaA	peroxide stress resistance protein YaaA
6401	snp	G	A	missense_variant c.59C>T p.Thr20Met	yaaA	peroxide stress resistance protein YaaA
317737	snp	T	C	missense_variant c.583A>G p.Thr195Ala	rclC	reactive chlorine species resistance protein C
318076	snp	T	A	missense_variant c.244A>T p.Thr82Ser	rclC	reactive chlorine species resistance protein C
318301	snp	G	T	missense_variant c.19C>A p.Leu7Met	rclC	reactive chlorine species resistance protein C
1007587	snp	A	G	missense_variant c.14T>C p.Ile5Thr	ycbX	6-N-hydroxylaminopurine resistance protein
1007596	snp	G	A	missense_variant c.5C>T p.Ala2Val	ycbX	6-N-hydroxylaminopurine resistance protein
1620120	snp	C	A	missense_variant c.132C>A p.His44Gln	marB	multiple antibiotic resistance protein
2227335	snp	C	A	missense_variant c.1424G>T p.Gly475Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227368	snp	G	A	missense_variant c.1391C>T p.Pro464Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227545	snp	C	A	missense_variant c.1214G>T p.Trp405Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228331	snp	A	T	missense_variant c.428T>A p.Val143Glu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228349	snp	G	A	missense_variant c.410C>T p.Ala137Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228433	snp	C	A	missense_variant c.326G>T p.Arg109Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228463	snp	G	A	missense_variant c.296C>T p.Pro99Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
3869713	snp	G	A	missense_variant c.337G>A p.Ala113Thr	cbrA	colicin M resistance protein
3869965	snp	T	G	missense_variant c.589T>G p.Ser197Ala	cbrA	colicin M resistance protein
3869974	snp	A	G	missense_variant c.598A>G p.Asn200Asp	cbrA	colicin M resistance protein
3870106	snp	A	G	missense_variant c.730A>G p.Thr244Ala	cbrA	colicin M resistance protein
3870253	snp	A	G	missense_variant c.877A>G p.Thr293Ala	cbrA	colicin M resistance protein
3870412	snp	G	A	missense_variant c.1036G>A p.Val346Met	cbrA	colicin M resistance protein
4103027	snp	C	T	missense_variant c.206C>T p.Ala69Val	yiiM	2-amino-6-N-hydroxylaminopurine resistance protein
4103116	snp	T	C	missense_variant c.295T>C p.Tyr99His	yiiM	2-amino-6-N-hydroxylaminopurine resistance protein

ID231

GenomePosition	Type	ReferenceAllele	AlternateAllele	Consequence	AffectedGene	Product
6239	snp	G	T	missense_variant c.221C>A p.Ala74Glu	yaaA	peroxide stress resistance protein YaaA
6401	snp	G	A	missense_variant c.59C>T p.Thr20Met	yaaA	peroxide stress resistance protein YaaA
317737	snp	T	C	missense_variant c.583A>G p.Thr195Ala	rclC	reactive chlorine species resistance protein C
318076	snp	T	A	missense_variant c.244A>T p.Thr82Ser	rclC	reactive chlorine species resistance protein C
318301	snp	G	T	missense_variant c.19C>A p.Leu7Met	rclC	reactive chlorine species resistance protein C
1007587	snp	A	G	missense_variant c.14T>C p.Ile5Thr	ycbX	6-N-hydroxylaminopurine resistance protein
1007596	snp	G	A	missense_variant c.5C>T p.Ala2Val	ycbX	6-N-hydroxylaminopurine resistance protein
1620120	snp	C	A	missense_variant c.132C>A p.His44Gln	marB	multiple antibiotic resistance protein
2227335	snp	C	A	missense_variant c.1424G>T p.Gly475Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227368	snp	G	A	missense_variant c.1391C>T p.Pro464Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227545	snp	C	A	missense_variant c.1214G>T p.Trp405Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228331	snp	A	T	missense_variant c.428T>A p.Val143Glu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228349	snp	G	A	missense_variant c.410C>T p.Ala137Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228433	snp	C	A	missense_variant c.326G>T p.Arg109Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228463	snp	G	A	missense_variant c.296C>T p.Pro99Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2630599	snp	T	A	missense_variant c.274T>A p.Ser92Thr	yfgI	nalidixic acid resistance protein YfgI
2630850	snp	C	A	missense_variant c.525C>A p.Asp175Glu	yfgI	nalidixic acid resistance protein YfgI
3869486	snp	G	A	missense_variant c.110G>A p.Cys37Tyr	cbrA	colicin M resistance protein
3869713	snp	G	A	missense_variant c.337G>A p.Ala113Thr	cbrA	colicin M resistance protein
3870106	snp	A	G	missense_variant c.730A>G p.Thr244Ala	cbrA	colicin M resistance protein
3870253	snp	A	G	missense_variant c.877A>G p.Thr293Ala	cbrA	colicin M resistance protein
3870268	snp	T	G	missense_variant c.892T>G p.Ser298Ala	cbrA	colicin M resistance protein
3870412	snp	G	A	missense_variant c.1036G>A p.Val346Met	cbrA	colicin M resistance protein
4103027	snp	C	T	missense_variant c.206C>T p.Ala69Val	yiiM	2-amino-6-N-hydroxylaminopurine resistance protein
4103116	snp	T	C	missense_variant c.295T>C p.Tyr99His	yiiM	2-amino-6-N-hydroxylaminopurine resistance protein

ID233

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GenomePosition	Type	ReferenceAllele	AlternateAllele	Consequence	AffectedGene	Product
6239	snp	G	T	missense_variant c.221C>A p.Ala74Glu	yaaA	peroxide stress resistance protein YaaA
6401	snp	G	A	missense_variant c.59C>T p.Thr20Met	yaaA	peroxide stress resistance protein YaaA
317737	snp	T	C	missense_variant c.583A>G p.Thr195Ala	rclC	reactive chlorine species resistance protein C
318076	snp	T	A	missense_variant c.244A>T p.Thr82Ser	rclC	reactive chlorine species resistance protein C
318301	snp	G	T	missense_variant c.19C>A p.Leu7Met	rclC	reactive chlorine species resistance protein C
1007587	snp	A	G	missense_variant c.14T>C p.Ile5Thr	ycbX	6-N-hydroxylaminopurine resistance protein
1007596	snp	G	A	missense_variant c.5C>T p.Ala2Val	ycbX	6-N-hydroxylaminopurine resistance protein
1620120	snp	C	A	missense_variant c.132C>A p.His44Gln	marB	multiple antibiotic resistance protein
2227335	snp	C	A	missense_variant c.1424G>T p.Gly475Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227368	snp	G	A	missense_variant c.1391C>T p.Pro464Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227545	snp	C	A	missense_variant c.1214G>T p.Trp405Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228331	snp	A	T	missense_variant c.428T>A p.Val143Glu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228349	snp	G	A	missense_variant c.410C>T p.Ala137Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228433	snp	C	A	missense_variant c.326G>T p.Arg109Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228463	snp	G	A	missense_variant c.296C>T p.Pro99Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2630599	snp	T	A	missense_variant c.274T>A p.Ser92Thr	yfgI	nalidixic acid resistance protein YfgI
2630850	snp	C	A	missense_variant c.525C>A p.Asp175Glu	yfgI	nalidixic acid resistance protein YfgI
3869486	snp	G	A	missense_variant c.110G>A p.Cys37Tyr	cbrA	colicin M resistance protein
3869713	snp	G	A	missense_variant c.337G>A p.Ala113Thr	cbrA	colicin M resistance protein
3870106	snp	A	G	missense_variant c.730A>G p.Thr244Ala	cbrA	colicin M resistance protein
3870253	snp	A	G	missense_variant c.877A>G p.Thr293Ala	cbrA	colicin M resistance protein
3870268	snp	T	G	missense_variant c.892T>G p.Ser298Ala	cbrA	colicin M resistance protein
3870412	snp	G	A	missense_variant c.1036G>A p.Val346Met	cbrA	colicin M resistance protein
4103027	snp	C	T	missense_variant c.206C>T p.Ala69Val	yiiM	2-amino-6-N-hydroxylaminopurine resistance protein
4103116	snp	T	C	missense_variant c.295T>C p.Tyr99His	yiiM	2-amino-6-N-hydroxylaminopurine resistance protein

ID235

GenomePosition	Type	ReferenceAllele	AlternateAllele	Consequence	AffectedGene	Product
6239	snp	G	T	missense_variant c.221C>A p.Ala74Glu	yaaA	peroxide stress resistance protein YaaA
317780	snp	T	A	missense_variant c.540A>T p.Glu180Asp	rclC	reactive chlorine species resistance protein C
318076	snp	T	A	missense_variant c.244A>T p.Thr82Ser	rclC	reactive chlorine species resistance protein C
743269	snp	C	T	missense_variant c.443C>T p.Ala148Val	ybgI	radiation resistance protein YbgI
1007042	snp	G	T	missense_variant c.559C>A p.Arg187Ser	ycbX	6-N-hydroxylaminopurine resistance protein
1007428	snp	G	A	missense_variant c.173C>T p.Thr58Ile	ycbX	6-N-hydroxylaminopurine resistance protein
1007587	snp	A	G	missense_variant c.14T>C p.Ile5Thr	ycbX	6-N-hydroxylaminopurine resistance protein
1216402	snp	A	G	missense_variant c.34A>G p.Thr12Ala	ariR	regulator of acid resistance, influenced by indole
1216417	snp	G	T	missense_variant c.49G>T p.Ala17Ser	ariR	regulator of acid resistance, influenced by indole
1216562	snp	G	A	missense_variant c.194G>A p.Ser65Asn	ariR	regulator of acid resistance, influenced by indole
1500615	snp	G	A	missense_variant c.43G>A p.Gly15Ser	tehA	tellurite resistance protein
1500741	snp	A	G	missense_variant c.169A>G p.Ser57Gly	tehA	tellurite resistance protein
1500753	snp	G	A	missense_variant c.181G>A p.Ala61Thr	tehA	tellurite resistance protein
1501399	snp	G	T	missense_variant c.827G>T p.Ser276Ile	tehA	tellurite resistance protein
1501518	snp	G	A	missense_variant c.946G>A p.Val316Ile	tehA	tellurite resistance protein
1620002	snp	C	T	missense_variant c.14C>T p.Ser5Leu	marB	multiple antibiotic resistance protein
1620120	snp	C	A	missense_variant c.132C>A p.His44Gln	marB	multiple antibiotic resistance protein
2227335	snp	C	A	missense_variant c.1424G>T p.Gly475Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227353	snp	A	G	missense_variant c.1406T>C p.Leu469Pro	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227510	snp	C	T	missense_variant c.1249G>A p.Ala417Thr	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227560	snp	A	G	missense_variant c.1199T>C p.Val400Ala	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227566	snp	T	C	missense_variant c.1193A>G p.Gln398Arg	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227653	snp	A	G	missense_variant c.1106T>C p.Ile369Thr	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227872	snp	G	C	missense_variant c.887C>G p.Pro296Arg	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227935	snp	T	A	missense_variant c.824A>T p.Asn275Ile	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227949	snp	A	C	missense_variant c.810T>G p.Ser270Arg	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228109	snp	C	G	missense_variant c.650G>C p.Arg217Pro	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228239	snp	G	A	missense_variant c.520C>T p.Arg174Trp	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228265	snp	G	A	missense_variant c.494C>T p.Pro165Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228349	snp	G	A	missense_variant c.410C>T p.Ala137Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228367	snp	C	A	missense_variant c.392G>T p.Arg131Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228397	snp	G	C	missense_variant c.362C>G p.Ala121Gly	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228433	snp	C	A	missense_variant c.326G>T p.Arg109Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2630364	snp	A	T	missense_variant c.39A>T p.Leu13Phe	yfgI	nalidixic acid resistance protein YfgI
2630599	snp	T	A	missense_variant c.274T>A p.Ser92Thr	yfgI	nalidixic acid resistance protein YfgI
3635534	snp	T	A	missense_variant c.694T>A p.Phe232Ile	yhiM	inner membrane protein with a role in acid resistance
3635595	snp	C	T	missense_variant c.755C>T p.Ala252Val	yhiM	inner membrane protein with a role in acid resistance
3869965	snp	T	G	missense_variant c.589T>G p.Ser197Ala	cbrA	colicin M resistance protein
3869974	snp	A	G	missense_variant c.598A>G p.Asn200Asp	cbrA	colicin M resistance protein
3870080	snp	G	A	missense_variant c.704G>A p.Ser235Asn	cbrA	colicin M resistance protein
3870253	snp	A	G	missense_variant c.877A>G p.Thr293Ala	cbrA	colicin M resistance protein
3870258	snp	C	G	missense_variant c.882C>G p.Asp294Glu	cbrA	colicin M resistance protein
3870295	snp	C	A	missense_variant c.919C>A p.Leu307Ile	cbrA	colicin M resistance protein
4102964	snp	A	T	missense_variant c.143A>T p.Lys48Met	yiiM	2-amino-6-N-hydroxylaminopurine resistance protein

ID237

GenomePosition	Type	ReferenceAllele	AlternateAllele	Consequence	AffectedGene	Product
6239	snp	G	T	missense_variant c.221C>A p.Ala74Glu	yaaA	peroxide stress resistance protein YaaA
6401	snp	G	A	missense_variant c.59C>T p.Thr20Met	yaaA	peroxide stress resistance protein YaaA
303055	snp	T	A	missense_variant c.65T>A p.Leu22Gln	yagU	inner membrane protein that contributes to acid resistance
317737	snp	T	C	missense_variant c.583A>G p.Thr195Ala	rclC	reactive chlorine species resistance protein C
318076	snp	T	A	missense_variant c.244A>T p.Thr82Ser	rclC	reactive chlorine species resistance protein C
318301	snp	G	T	missense_variant c.19C>A p.Leu7Met	rclC	reactive chlorine species resistance protein C
1007587	snp	A	G	missense_variant c.14T>C p.Ile5Thr	ycbX	6-N-hydroxylaminopurine resistance protein
1007596	snp	G	A	missense_variant c.5C>T p.Ala2Val	ycbX	6-N-hydroxylaminopurine resistance protein
1620120	snp	C	A	missense_variant c.132C>A p.His44Gln	marB	multiple antibiotic resistance protein
2227335	snp	C	A	missense_variant c.1424G>T p.Gly475Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227368	snp	G	A	missense_variant c.1391C>T p.Pro464Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227545	snp	C	A	missense_variant c.1214G>T p.Trp405Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228331	snp	A	T	missense_variant c.428T>A p.Val143Glu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228349	snp	G	A	missense_variant c.410C>T p.Ala137Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228433	snp	C	A	missense_variant c.326G>T p.Arg109Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228463	snp	G	A	missense_variant c.296C>T p.Pro99Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
3869713	snp	G	A	missense_variant c.337G>A p.Ala113Thr	cbrA	colicin M resistance protein
3869965	snp	T	G	missense_variant c.589T>G p.Ser197Ala	cbrA	colicin M resistance protein
3869974	snp	A	G	missense_variant c.598A>G p.Asn200Asp	cbrA	colicin M resistance protein
3870106	snp	A	G	missense_variant c.730A>G p.Thr244Ala	cbrA	colicin M resistance protein
3870253	snp	A	G	missense_variant c.877A>G p.Thr293Ala	cbrA	colicin M resistance protein
3870412	snp	G	A	missense_variant c.1036G>A p.Val346Met	cbrA	colicin M resistance protein
4103027	snp	C	T	missense_variant c.206C>T p.Ala69Val	yiiM	2-amino-6-N-hydroxylaminopurine resistance protein
4103116	snp	T	C	missense_variant c.295T>C p.Tyr99His	yiiM	2-amino-6-N-hydroxylaminopurine resistance protein

ID256

GenomePosition	Type	ReferenceAllele	AlternateAllele	Consequence	AffectedGene	Product
5732	snp	T	G	missense_variant c.728A>C p.Asp243Ala	yaaA	peroxide stress resistance protein YaaA
6239	snp	G	T	missense_variant c.221C>A p.Ala74Glu	yaaA	peroxide stress resistance protein YaaA
6408	snp	T	G	missense_variant c.52A>C p.Thr18Pro	yaaA	peroxide stress resistance protein YaaA
317780	snp	T	A	missense_variant c.540A>T p.Glu180Asp	rclC	reactive chlorine species resistance protein C
318312	snp	T	C	missense_variant c.8A>G p.Lys3Arg	rclC	reactive chlorine species resistance protein C
742927	snp	C	T	missense_variant c.101C>T p.Thr34Met	ybgI	radiation resistance protein YbgI
1006777	snp	G	C	missense_variant c.824C>G p.Ala275Gly	ycbX	6-N-hydroxylaminopurine resistance protein
1006933	snp	C	T	missense_variant c.668G>A p.Gly223Asp	ycbX	6-N-hydroxylaminopurine resistance protein
1007042	snp	G	T	missense_variant c.559C>A p.Arg187Ser	ycbX	6-N-hydroxylaminopurine resistance protein
1007131	snp	T	G	missense_variant c.470A>C p.Asp157Ala	ycbX	6-N-hydroxylaminopurine resistance protein
1007587	snp	A	G	missense_variant c.14T>C p.Ile5Thr	ycbX	6-N-hydroxylaminopurine resistance protein
1216402	snp	A	T	missense_variant c.34A>T p.Thr12Ser	ariR	regulator of acid resistance, influenced by indole
1216417	snp	G	T	missense_variant c.49G>T p.Ala17Ser	ariR	regulator of acid resistance, influenced by indole
1441685	snp	T	C	missense_variant c.59A>G p.Asn20Ser	hslJ	lipoprotein implicated in Novobiocin resistance
1441725	snp	A	G	missense_variant c.19T>C p.Phe7Leu	hslJ	lipoprotein implicated in Novobiocin resistance
1500741	snp	A	G	missense_variant c.169A>G p.Ser57Gly	tehA	tellurite resistance protein
1500753	snp	G	A	missense_variant c.181G>A p.Ala61Thr	tehA	tellurite resistance protein
1620002	snp	C	T	missense_variant c.14C>T p.Ser5Leu	marB	multiple antibiotic resistance protein
1620016	snp	G	A	missense_variant c.28G>A p.Ala10Thr	marB	multiple antibiotic resistance protein
1620086	snp	C	G	missense_variant c.98C>G p.Ala33Gly	marB	multiple antibiotic resistance protein
1620120	snp	C	A	missense_variant c.132C>A p.His44Gln	marB	multiple antibiotic resistance protein
2227335	snp	C	A	missense_variant c.1424G>T p.Gly475Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227452	snp	A	C	missense_variant c.1307T>G p.Leu436Arg	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227653	snp	A	G	missense_variant c.1106T>C p.Ile369Thr	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227818	snp	G	A	missense_variant c.941C>T p.Pro314Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227908	snp	G	A	missense_variant c.851C>T p.Ala284Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227935	snp	T	A	missense_variant c.824A>T p.Asn275Ile	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227949	snp	A	C	missense_variant c.810T>G p.Ser270Arg	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228109	snp	C	G	missense_variant c.650G>C p.Arg217Pro	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228145	snp	C	T	missense_variant c.614G>A p.Cys205Tyr	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228151	snp	C	A	missense_variant c.608G>T p.Arg203Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228241	snp	C	T	missense_variant c.518G>A p.Gly173Glu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228265	snp	G	A	missense_variant c.494C>T p.Pro165Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228277	snp	C	T	missense_variant c.482G>A p.Arg161Gln	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228349	snp	G	A	missense_variant c.410C>T p.Ala137Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228367	snp	C	A	missense_variant c.392G>T p.Arg131Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228397	snp	G	C	missense_variant c.362C>G p.Ala121Gly	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228406	snp	C	A	missense_variant c.353G>T p.Arg118Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228433	snp	C	A	missense_variant c.326G>T p.Arg109Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228463	snp	G	A	missense_variant c.296C>T p.Pro99Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2630599	snp	T	A	missense_variant c.274T>A p.Ser92Thr	yfgI	nalidixic acid resistance protein YfgI
3869965	snp	T	G	missense_variant c.589T>G p.Ser197Ala	cbrA	colicin M resistance protein
3869974	snp	A	G	missense_variant c.598A>G p.Asn200Asp	cbrA	colicin M resistance protein
3870106	snp	A	G	missense_variant c.730A>G p.Thr244Ala	cbrA	colicin M resistance protein
3870253	snp	A	G	missense_variant c.877A>G p.Thr293Ala	cbrA	colicin M resistance protein
3870258	snp	C	G	missense_variant c.882C>G p.Asp294Glu	cbrA	colicin M resistance protein
4102929	snp	G	C	missense_variant c.108G>C p.Glu36Asp	yiiM	2-amino-6-N-hydroxylaminopurine resistance protein

ID263

GenomePosition	Type	ReferenceAllele	AlternateAllele	Consequence	AffectedGene	Product
5732	snp	T	G	missense_variant c.728A>C p.Asp243Ala	yaaA	peroxide stress resistance protein YaaA
6162	snp	C	T	missense_variant c.298G>A p.Asp100Asn	yaaA	peroxide stress resistance protein YaaA
6239	snp	G	T	missense_variant c.221C>A p.Ala74Glu	yaaA	peroxide stress resistance protein YaaA
1007266	snp	C	T	missense_variant c.335G>A p.Gly112Glu	ycbX	6-N-hydroxylaminopurine resistance protein
2227335	snp	C	A	missense_variant c.1424G>T p.Gly475Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228170	snp	G	A	missense_variant c.589C>T p.Pro197Ser	mdtQ	putative multidrug resistance outer membrane protein MdtQ

ID282

GenomePosition	Type	ReferenceAllele	AlternateAllele	Consequence	AffectedGene	Product
5732	snp	T	G	missense_variant c.728A>C p.Asp243Ala	yaaA	peroxide stress resistance protein YaaA
6239	snp	G	T	missense_variant c.221C>A p.Ala74Glu	yaaA	peroxide stress resistance protein YaaA
1620002	snp	C	T	missense_variant c.14C>T p.Ser5Leu	marB	multiple antibiotic resistance protein
2227335	snp	C	A	missense_variant c.1424G>T p.Gly475Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
3869974	snp	A	G	missense_variant c.598A>G p.Asn200Asp	cbrA	colicin M resistance protein
3870253	snp	A	G	missense_variant c.877A>G p.Thr293Ala	cbrA	colicin M resistance protein
3870258	snp	C	G	missense_variant c.882C>G p.Asp294Glu	cbrA	colicin M resistance protein

ORTHO013EI

## Error in read.table("ORTHO013EI_amr_snps", header = T, sep = "\t", dec = ".", : no lines available in input

GenomePosition	Type	ReferenceAllele	AlternateAllele	Consequence	AffectedGene	Product
5732	snp	T	G	missense_variant c.728A>C p.Asp243Ala	yaaA	peroxide stress resistance protein YaaA
6239	snp	G	T	missense_variant c.221C>A p.Ala74Glu	yaaA	peroxide stress resistance protein YaaA
1620002	snp	C	T	missense_variant c.14C>T p.Ser5Leu	marB	multiple antibiotic resistance protein
2227335	snp	C	A	missense_variant c.1424G>T p.Gly475Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
3869974	snp	A	G	missense_variant c.598A>G p.Asn200Asp	cbrA	colicin M resistance protein
3870253	snp	A	G	missense_variant c.877A>G p.Thr293Ala	cbrA	colicin M resistance protein
3870258	snp	C	G	missense_variant c.882C>G p.Asp294Glu	cbrA	colicin M resistance protein

ORTHO055E

## Error in read.table("ORTHO055E_amr_snps", header = T, sep = "\t", dec = ".", : no lines available in input

GenomePosition	Type	ReferenceAllele	AlternateAllele	Consequence	AffectedGene	Product
5732	snp	T	G	missense_variant c.728A>C p.Asp243Ala	yaaA	peroxide stress resistance protein YaaA
6239	snp	G	T	missense_variant c.221C>A p.Ala74Glu	yaaA	peroxide stress resistance protein YaaA
1620002	snp	C	T	missense_variant c.14C>T p.Ser5Leu	marB	multiple antibiotic resistance protein
2227335	snp	C	A	missense_variant c.1424G>T p.Gly475Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
3869974	snp	A	G	missense_variant c.598A>G p.Asn200Asp	cbrA	colicin M resistance protein
3870253	snp	A	G	missense_variant c.877A>G p.Thr293Ala	cbrA	colicin M resistance protein
3870258	snp	C	G	missense_variant c.882C>G p.Asp294Glu	cbrA	colicin M resistance protein

ORTHO082EI

GenomePosition	Type	ReferenceAllele	AlternateAllele	Consequence	AffectedGene	Product
743510	snp	G	TRUE	missense_variant c.684G>T p.Glu228Asp	ybgI	radiation resistance protein YbgI

ORTHO08HW

GenomePosition	Type	ReferenceAllele	AlternateAllele	Consequence	AffectedGene	Product
5732	snp	T	G	missense_variant c.728A>C p.Asp243Ala	yaaA	peroxide stress resistance protein YaaA
6239	snp	G	T	missense_variant c.221C>A p.Ala74Glu	yaaA	peroxide stress resistance protein YaaA
6401	snp	G	A	missense_variant c.59C>T p.Thr20Met	yaaA	peroxide stress resistance protein YaaA
318076	snp	T	A	missense_variant c.244A>T p.Thr82Ser	rclC	reactive chlorine species resistance protein C
1007587	snp	A	G	missense_variant c.14T>C p.Ile5Thr	ycbX	6-N-hydroxylaminopurine resistance protein
1500753	snp	G	A	missense_variant c.181G>A p.Ala61Thr	tehA	tellurite resistance protein
1620120	snp	C	A	missense_variant c.132C>A p.His44Gln	marB	multiple antibiotic resistance protein
2227335	snp	C	A	missense_variant c.1424G>T p.Gly475Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227368	snp	G	A	missense_variant c.1391C>T p.Pro464Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2227545	snp	C	A	missense_variant c.1214G>T p.Trp405Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228331	snp	A	T	missense_variant c.428T>A p.Val143Glu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228349	snp	G	A	missense_variant c.410C>T p.Ala137Val	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228433	snp	C	A	missense_variant c.326G>T p.Arg109Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2228463	snp	G	A	missense_variant c.296C>T p.Pro99Leu	mdtQ	putative multidrug resistance outer membrane protein MdtQ
2630450	snp	G	A	missense_variant c.125G>A p.Arg42Lys	yfgI	nalidixic acid resistance protein YfgI
3869713	snp	G	A	missense_variant c.337G>A p.Ala113Thr	cbrA	colicin M resistance protein
3869921	snp	C	T	missense_variant c.545C>T p.Ala182Val	cbrA	colicin M resistance protein
3870106	snp	A	G	missense_variant c.730A>G p.Thr244Ala	cbrA	colicin M resistance protein
3870253	snp	A	G	missense_variant c.877A>G p.Thr293Ala	cbrA	colicin M resistance protein
3870412	snp	G	A	missense_variant c.1036G>A p.Val346Met	cbrA	colicin M resistance protein

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Phylogenetic inference

Phylogenetic inference based on vcf SNPS

Rectangular (phylogram)

Circular (phylogram)

Circular (cladogram)

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Antimicrobial Resistance Profiling

Field	Description
Contig	Contig name where the gene was found
Start	Start position of the gene within the contig
End	End position of the gene within the contig
Gene	Antibiotic resistance gene
Gaps	Gaps in subject (genome) and query (antibiotic resistance gene)
Coverage	Proportion (%) of the gene covered
Identity	Proportion (%) of exact nucleotide matches
Accession	Accesion number of the antibiotic resistance gene
Product	Antibiotic resistance gene product
Resistance	Antibiotic that the gene confers resistance to

Select the samples and the database

ID002

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00128	1695	2555	aac(3)-IIa_1	0/0	100.0	99.8	X51534	aac(3)-IIa	Gentamicin, Tobramycin
contig00138	1539	2138	aac(6’)-Ib-cr_1	0/0	100.0	100.0	DQ303918	aac(6’)-Ib-cr	Ciprofloxacin
contig00095	6564	7367	aph(3’’)-Ib_5	0/0	100.0	100.0	AF321551	aph(3’’)-Ib	Streptomycin
contig00095	5728	6564	aph(6)-Id_1	0/0	100.0	100.0	M28829	aph(6)-Id	Streptomycin
contig00095	450	1325	blaCTX-M-15_1	0/0	100.0	100.0	AY044436	blaCTX-M-15	Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig00052	16863	18008	blaMIR-1_1	0/0	100.0	99.5	M37839	blaMIR-1
contig00138	578	1408	blaOXA-1_1	0/0	100.0	100.0	HQ170510	blaOXA-1	Amoxicillin, Amoxicillin+Clavulanic_acid, Ampicillin, Ampicillin+Clavulanic_acid, Cefepime, Piperacillin, Piperacillin+Tazobactam
contig00095	4147	5007	blaTEM-1B_1	0/0	100.0	100.0	AY458016	blaTEM-1B	Amoxicillin, Ampicillin, Cephalothin, Piperacillin, Ticarcillin
contig00046	273	698	fosA_1	0/0	100.0	94.8	M85195	fosA	Fosfomycin
contig00095	7428	8243	sul2_2	0/0	100.0	100.0	AY034138	sul2	Sulfamethoxazole
contig00117	1429	2697	tet(A)_6	1/22	97.8	93.2	AF534183	tet(A)	Doxycycline, Tetracycline

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00128	1695	2555	AAC(3)-IIe	0/0	100.0	99.5	EU022315.1:0-861	AAC(3)-IIe is a plasmid-encoded aminoglycoside acetyltransferase in E. coli	aminoglycoside
contig00138	1539	2138	AAC(6’)-Ib-cr	0/0	100.0	100.0	DQ303918:0-600	AAC(6’)-Ib-cr is an aminoglycoside acetyltransferase encoded by plasmids transposons integrons in Enterobacteriaceae. The aac(6’)-Ib-cr variant gene can induce resistance against aminoglycoside and fluoroquinolone simultaneously	aminoglycoside, fluoroquinolone
contig00095	6564	7367	APH(3’’)-Ib	0/0	100.0	99.8	AF313472:15593-16397	APH(3’’)-Ib is an aminoglycoside phosphotransferase encoded by plasmids transposons integrative conjugative elements and chromosomes in Enterobacteriaceae and Pseudomonas spp.	aminoglycoside
contig00095	5728	6564	APH(6)-Id	0/0	100.0	99.9	AF024602:3155-3992	APH(6)-Id is an aminoglycoside phosphotransferase encoded by plasmids integrative conjugative elements and chromosomal genomic islands in K. pneumoniae Salmonella spp. E. coli Shigella flexneri Providencia alcalifaciens Pseudomonas spp. V. cholerae Edwardsiella tarda Pasteurella multocida and Aeromonas bestiarum	aminoglycoside
contig00095	450	1325	CTX-M-15	0/0	100.0	100.0	AY044436:1435-2311	CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family	cephalosporin
contig00007	7242	8435	Enterobacter_cloacae_acrA	0/0	100.0	99.5	DQ679966:299-1493	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. cloacae.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00046	273	698	FosA2	0/0	100.0	92.5	EU487198:216-642	An enzyme that confers resistance to fosfomycin in Enterobacter cloacae by breaking the epoxide ring of the molecule. It depends on the cofactors Manganese (II) and Potassium and uses Glutathione (GSH) as the nucleophilic molecule.	fosfomycin
contig00052	16863	18008	MIR-5	0/0	100.0	99.6	KP050484:0-1146	MIR-5 is a beta-lactamase. From the Lahey list of MIR beta-lactamases.	cephalosporin, monobactam
contig00138	578	1408	OXA-1	0/0	100.0	100.0	JN420336.1:2230-1399	OXA-1 is a beta-lactamase found in E. coli	cephalosporin, penam
contig00061	20573	20924	ramA	0/0	93.9	93.2	JQ727668:0-375	RamA (resistance antibiotic multiple) is a positive regulator of AcrAB-TolC and leads to high level multidrug resistance in Klebsiella pneumoniae Salmonella enterica and Enterobacter aerugenes increasing the expression of both the mar operon as well as AcrAB. RamA also decreases OmpF expression.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00095	7428	8243	sul2	0/0	100.0	100.0	AY055428.1:21084-20268	Sul2 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria usually found on small plasmids.	sulfonamide
contig00095	4147	5007	TEM-1	0/0	100.0	99.9	AL513383:161910-162771	TEM-1 is a broad-spectrum beta-lactamase found in many Gram-negative bacteria. Confers resistance to penicillins and first generation cephalosphorins.	cephalosporin, monobactam, penam, penem
contig00117	1429	2697	tet(A)	1/22	97.8	93.2	AF534183.1:2970-4245	TetA is a tetracycline efflux pump found in many species of Gram-negative bacteria.	tetracycline

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00128	1695	2555	(AGly)aac3-IIa	0/0	100.0	99.8	X51534:91-951	(AGly)aac3-IIa	NA
contig00095	6564	7367	(AGly)strA	0/0	100.0	99.9	AB366441:22458-23261	(AGly)strA	NA
contig00095	5728	6564	(AGly)strB	0/0	100.0	100.0	FJ474091:264-1100	(AGly)strB	NA
contig00095	450	1325	(Bla)blaCTX-M-15	0/0	100.0	100.0	JQ686199:261-1136	(Bla)blaCTX-M-15	NA
contig00052	16863	18008	(Bla)blaMIR-1	0/0	100.0	99.5	M37839:928-2073	(Bla)blaMIR-1	NA
contig00138	578	1408	(Bla)blaOXA-1	0/0	100.0	100.0	JQ682867:1-831	(Bla)blaOXA-1	NA
contig00095	4147	5007	(Bla)blaTEM-105	0/0	100.0	99.9	AF516720:215-1075	(Bla)blaTEM-105	NA
contig00046	273	698	(Fcyn)FosA2	0/0	100.0	92.5	EU487198:217-642	(Fcyn)FosA2	NA
contig00095	7428	8243	(Sul)sul2	0/0	100.0	100.0	EU360945:1617-2432	(Sul)sul2	NA
contig00117	1429	2725	(Tet)tetA	1/22	100.0	93.3	JX424423:94438-95712	(Tet)tetA	NA
contig00117	757	1398	(Tet)tetR	1/9	98.6	93.1	HF545434:53576-54226	(Tet)tetR	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00128	1695	2555	aac(3)-IIe	0/0	100	99.8	NG_047244.1	aminoglycoside N-acetyltransferase AAC(3)-IIe	GENTAMICIN
contig00138	1539	2093	aac(6’)-Ib-D181Y	0/0	100	99.8	NG_067946.1	AAC(6’)-Ib family aminoglycoside 6’-N-acetyltransferase	AMIKACIN, KANAMYCIN, TOBRAMYCIN
contig00095	6564	7391	aph(3’’)-Ib	0/0	100	100.0	NG_056002.2	aminoglycoside O-phosphotransferase APH(3’’)-Ib	STREPTOMYCIN
contig00095	5728	6564	aph(6)-Id	0/0	100	100.0	NG_047464.1	aminoglycoside O-phosphotransferase APH(6)-Id	STREPTOMYCIN
contig00095	450	1325	blaCTX-M-15	0/0	100	100.0	NG_048935.1	class A extended-spectrum beta-lactamase CTX-M-15	CEPHALOSPORIN
contig00052	16863	18008	blaMIR-1	0/0	100	99.5	NG_049293.1	cephalosporin-hydrolyzing class C beta-lactamase MIR-1	CEPHALOSPORIN
contig00138	578	1408	blaOXA-1	0/0	100	100.0	NG_049392.1	oxacillin-hydrolyzing class D beta-lactamase OXA-1	CEPHALOSPORIN
contig00095	4147	5007	blaTEM-1	0/0	100	100.0	NG_050145.1	class A broad-spectrum beta-lactamase TEM-1	BETA-LACTAM
contig00046	273	698	fosA	0/0	100	94.8	NG_050405.1	fosfomycin resistance glutathione transferase FosA	FOSFOMYCIN
contig00027	48688	51807	oqxB9	0/0	99	90.2	NG_050458.1	multidrug efflux RND transporter permease subunit OqxB9	PHENICOL, QUINOLONE
contig00095	7428	8243	sul2	0/0	100	100.0	NG_051852.1	sulfonamide-resistant dihydropteroate synthase Sul2	SULFONAMIDE
contig00117	1526	2725	tet(A)	0/0	100	100.0	NG_048157.1	tetracycline efflux MFS transporter Tet(A)	TETRACYCLINE

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00128	1695	2555	AAC3	0/0	100.0	99.8	MEG_44	Drugs:Aminoglycosides:Aminoglycoside_N-acetyltransferases:AAC3	NA
contig00007	7242	8435	ACRB	0/0	100.0	99.5	MEG_402	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRB	NA
contig00095	6564	7391	APH3-DPRIME	0/0	100.0	100.0	MEG_1019	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH3-DPRIME	NA
contig00095	5728	6564	APH6	0/0	100.0	100.0	MEG_1086	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH6	NA
contig00039	23432	24374	CTX	0/0	100.0	96.4	MEG_2435	Drugs:betalactams:Class_A_betalactamases:CTX	NA
contig00046	273	851	FOSA	1/1	99.5	93.1	MEG_2990	Drugs:Fosfomycin:Fosfomycin_thiol_transferases:FOSA	NA
contig00052	16862	18021	MIR	0/0	100.0	99.2	MEG_3972	Drugs:betalactams:Class_C_betalactamases:MIR	NA
contig00027	48688	51807	OQXB	0/0	99.0	90.2	MEG_4359	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:OQXB	NA
contig00138	578	1408	OXA	0/0	100.0	100.0	MEG_4980	Drugs:betalactams:Class_D_betalactamases:OXA	NA
contig00061	20573	20924	RAMA	0/0	93.9	93.2	MEG_6044	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:RAMA	NA
contig00095	7428	8243	SULII	0/0	100.0	100.0	MEG_6617	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULII	NA
contig00095	3780	5025	TEM	0/0	98.3	99.4	MEG_6875	Drugs:betalactams:Class_A_betalactamases:TEM	NA
contig00117	1526	2725	TETA	0/0	100.0	100.0	MEG_7021	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETA	NA

ID003

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00038	16686	17489	aph(3’’)-Ib_5	0/0	100.0	100.0	AF321551	aph(3’’)-Ib	Streptomycin
contig00038	15850	16686	aph(6)-Id_1	0/0	100.0	100.0	M28829	aph(6)-Id	Streptomycin
contig00038	10572	11447	blaCTX-M-15_1	0/0	100.0	100.0	AY044436	blaCTX-M-15	Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig00038	14269	15129	blaTEM-1B_1	0/0	100.0	100.0	AY458016	blaTEM-1B	Amoxicillin, Ampicillin, Cephalothin, Piperacillin, Ticarcillin
contig00060	182	664	dfrA14_5	0/0	100.0	99.6	DQ388123	dfrA14	Trimethoprim
contig00008	32402	33634	mdf(A)_1	0/0	100.0	98.1	Y08743	mdf(A)
contig00038	5275	5931	qnrS1_1	0/0	100.0	100.0	AB187515	qnrS1	Ciprofloxacin
contig00038	17550	18365	sul2_2	0/0	100.0	100.0	AY034138	sul2	Sulfamethoxazole
contig00059	1676	2922	tet(A)_6	0/0	97.8	100.0	AF534183	tet(A)	Doxycycline, Tetracycline

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00030	12982	16131	acrB	0/0	100.0	99.0	U00096.3:484403-481253	Protein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug/proton antiporter.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00010	134717	137830	acrD	0/0	100.0	98.8	AP009048.1:2586250-2589364	AcrD is an aminoglycoside efflux pump expressed in E. coli. Its expression can be induced by indole and is regulated by baeRS and cpxAR.	aminoglycoside
contig00001	501284	502441	acrE	0/0	100.0	98.4	U00096:3413863-3415021	AcrE is a membrane fusion protein similar to AcrA.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00001	502453	505557	acrF	0/0	100.0	97.8	U00096:3415032-3418137	AcrF is a inner membrane transporter similar to AcrB.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00001	500223	500885	acrS	0/0	100.0	98.9	U00096:3413465-3412802	AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.	cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00038	16686	17489	APH(3’’)-Ib	0/0	100.0	99.8	AF313472:15593-16397	APH(3’’)-Ib is an aminoglycoside phosphotransferase encoded by plasmids transposons integrative conjugative elements and chromosomes in Enterobacteriaceae and Pseudomonas spp.	aminoglycoside
contig00038	15850	16686	APH(6)-Id	0/0	100.0	99.9	AF024602:3155-3992	APH(6)-Id is an aminoglycoside phosphotransferase encoded by plasmids integrative conjugative elements and chromosomal genomic islands in K. pneumoniae Salmonella spp. E. coli Shigella flexneri Providencia alcalifaciens Pseudomonas spp. V. cholerae Edwardsiella tarda Pasteurella multocida and Aeromonas bestiarum	aminoglycoside
contig00001	300885	301704	bacA	0/0	99.8	96.2	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00002	12249	12970	baeR	0/0	99.9	97.0	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00002	10849	12252	baeS	0/0	100.0	92.2	AP009048:2165012-2166416	BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.	aminocoumarin, aminoglycoside
contig00020	22395	23768	cpxA	0/0	100.0	98.6	BA000007.3:4905062-4903688	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	aminocoumarin, aminoglycoside
contig00012	15391	16023	CRP	0/0	100.0	99.0	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00038	10572	11447	CTX-M-15	0/0	100.0	100.0	AY044436:1435-2311	CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family	cephalosporin
contig00060	182	664	dfrA14	0/0	100.0	99.8	EU780012:2162-2645	dfrA14 is an integron-encoded dihydrofolate reductase found in Escherichia coli	diaminopyrimidine
contig00013	60295	61467	emrA	0/0	100.0	98.0	AP009048:2810082-2811255	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	fluoroquinolone
contig00013	61484	63022	emrB	0/0	100.0	98.0	U00096:2812615-2814154	emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin.	fluoroquinolone
contig00002	319173	320228	emrK	0/0	100.0	97.8	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00013	59638	60168	emrR	0/0	100.0	99.4	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00002	317635	319173	emrY	0/0	100.0	97.5	D78168:1591-3130	emrY is a multidrug transport that moves substrates across the inner membrane of the Gram-negative E. coli. It is a homolog of emrB.	tetracycline
contig00006	116765	118408	eptA	0/0	100.0	98.2	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00030	16154	17347	Escherichia_coli_acrA	0/0	100.0	99.2	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00006	160327	161460	Escherichia_coli_ampC	0/0	100.0	97.6	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00002	382511	383815	Escherichia_coli_ampC1_beta-lactamase	0/0	100.0	96.0	FN649414.1:2765050-2766355	An ampC-like beta-lactamase identified from Escherichia coli.	cephalosporin, penam
contig00009	24731	25888	Escherichia_coli_ampH	0/0	100.0	96.9	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig00008	32402	33634	Escherichia_coli_mdfA	0/0	100.0	96.6	JQ394987:0-1233	Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter.	benzalkonium_chloride, rhodamine, tetracycline
contig00002	320752	321366	evgA	0/0	100.0	99.0	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00002	321371	324964	evgS	0/0	100.0	96.8	U00096:2484373-2487967	EvgS is a sensor protein that phosphorylates the regulatory protein EvgA. evgS corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	fluoroquinolone, macrolide, penam, tetracycline
contig00029	54225	54953	gadW	0/0	100.0	95.6	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig00029	55322	56146	gadX	0/0	100.0	94.3	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00005	190729	191142	H-NS	0/0	100.0	99.5	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00014	7736	8413	kdpE	0/0	100.0	95.4	U00096.3:721733-721055	kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding.	aminoglycoside
contig00023	62120	62503	marA	0/0	100.0	99.5	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00002	1989	3236	mdtA	0/0	100.0	96.5	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00002	3236	6358	mdtB	0/0	100.0	96.9	U00096:2155262-2158385	MdtB is a transporter that forms a heteromultimer complex with MdtC to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex.	aminocoumarin
contig00002	6359	9436	mdtC	0/0	100.0	96.7	U00096:2158385-2161463	MdtC is a transporter that forms a heteromultimer complex with MdtB to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex. In the absence of MdtB MdtC can form a homomultimer complex that results in a functioning efflux complex with a narrower drug specificity. mdtC corresponds to 3 loci in Pseudomonas aeruginosa PAO1 (gene name: muxC/muxB) and 3 loci in Pseudomonas aeruginosa LESB58.	aminocoumarin
contig00029	49567	50724	mdtE	0/0	100.0	98.8	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00029	50749	53862	mdtF	0/0	100.0	98.5	U00096:3660413-3663527	MdtF is the multidrug inner membrane transporter for the MdtEF-TolC efflux complex.	fluoroquinolone, macrolide, penam
contig00003	83168	84394	mdtG	0/0	100.0	98.5	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00003	73329	74537	mdtH	0/0	100.0	97.8	U00096:1125326-1124117	Multidrug resistance protein MdtH	fluoroquinolone
contig00007	170444	171676	mdtM	0/0	100.0	96.5	U00096.3:4568519-4567286	Multidrug resistance protein MdtM	acridine_dye, fluoroquinolone, lincosamide, nucleoside, phenicol
contig00006	93066	94097	mdtN	0/0	100.0	96.4	AP009048.1:4307588-4306556	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	acridine_dye, nucleoside
contig00006	91015	93066	mdtO	0/0	100.0	96.3	AP009048.1:4306557-4304505	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00006	89552	91018	mdtP	0/0	100.0	97.5	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00010	113536	114010	mphB	0/0	99.6	96.6	AE005174.2:3397370-3397847	The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides.	macrolide
contig00003	217787	219535	msbA	0/0	100.0	99.0	U00096.3:966620-968369	MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability.	nitroimidazole
contig00002	215066	216034	pmrF	0/0	100.0	98.1	U00096:2367070-2368039	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide
contig00038	5275	5931	QnrS1	0/0	100.0	100.0	DQ485529.1:0-657	QnrS1 is a plasmid-mediated quinolone resistance protein found in Shigella flexneri	fluoroquinolone
contig00038	17550	18365	sul2	0/0	100.0	100.0	AY055428.1:21084-20268	Sul2 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria usually found on small plasmids.	sulfonamide
contig00038	14269	15129	TEM-1	0/0	100.0	99.9	AL513383:161910-162771	TEM-1 is a broad-spectrum beta-lactamase found in many Gram-negative bacteria. Confers resistance to penicillins and first generation cephalosphorins.	cephalosporin, monobactam, penam, penem
contig00059	1676	2922	tet(A)	0/0	97.8	100.0	AF534183.1:2970-4245	TetA is a tetracycline efflux pump found in many species of Gram-negative bacteria.	tetracycline
contig00001	278685	280172	tolC	0/0	100.0	98.5	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan
contig00015	53196	54362	ugd	0/0	100.0	97.3	U00096:2099613-2098446	PmrE is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin	peptide
contig00002	151927	153570	yojI	0/0	100.0	97.5	U00096.3:2308615-2306971	YojI mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. YojI is capable of pumping out microcin molecules. The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI.	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00038	16686	17489	(AGly)strA	0/0	100	99.9	AB366441:22458-23261	(AGly)strA	NA
contig00038	15850	16686	(AGly)strB	0/0	100	100.0	FJ474091:264-1100	(AGly)strB	NA
contig00002	382511	383815	(Bla)AmpC1_Ecoli	0/0	100	96.0	FN649414:2765051-2766355	(Bla)AmpC1_Ecoli	NA
contig00006	160327	161460	(Bla)AmpC2_Ecoli	0/0	100	97.6	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00009	24731	25888	(Bla)ampH_Ecoli	0/0	100	96.9	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00038	10572	11447	(Bla)blaCTX-M-15	0/0	100	100.0	JQ686199:261-1136	(Bla)blaCTX-M-15	NA
contig00038	14269	15129	(Bla)blaTEM-105	0/0	100	99.9	AF516720:215-1075	(Bla)blaTEM-105	NA
contig00014	50257	52158	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100	99.0	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA
contig00038	5275	5931	(Flq)qnr-S1	0/0	100	100.0	AB187515:9737-10393	(Flq)qnr-S1	NA
contig00038	17550	18365	(Sul)sul2	0/0	100	100.0	EU360945:1617-2432	(Sul)sul2	NA
contig00059	1648	2922	(Tet)tetA	0/0	100	100.0	JX424423:94438-95712	(Tet)tetA	NA
contig00060	182	655	(Tmt)dfrA14	0/0	100	100.0	GU726917:72-545	(Tmt)dfrA14	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00038	16686	17513	aph(3’’)-Ib	0/0	100	100.0	NG_056002.2	aminoglycoside O-phosphotransferase APH(3’’)-Ib	STREPTOMYCIN
contig00038	15850	16686	aph(6)-Id	0/0	100	100.0	NG_047464.1	aminoglycoside O-phosphotransferase APH(6)-Id	STREPTOMYCIN
contig00038	10572	11447	blaCTX-M-15	0/0	100	100.0	NG_048935.1	class A extended-spectrum beta-lactamase CTX-M-15	CEPHALOSPORIN
contig00006	160327	161460	blaEC-8	0/0	100	98.2	NG_049086.1	cephalosporin-hydrolyzing class C beta-lactamase EC-8	CEPHALOSPORIN
contig00038	14269	15129	blaTEM-1	0/0	100	100.0	NG_050145.1	class A broad-spectrum beta-lactamase TEM-1	BETA-LACTAM
contig00060	182	655	dfrA14	0/0	100	100.0	NG_056035.1	trimethoprim-resistant dihydrofolate reductase DfrA14	TRIMETHOPRIM
contig00038	5275	5931	qnrS1	0/0	100	100.0	NG_050543.1	quinolone resistance pentapeptide repeat protein QnrS1	QUINOLONE
contig00038	17550	18365	sul2	0/0	100	100.0	NG_051852.1	sulfonamide-resistant dihydropteroate synthase Sul2	SULFONAMIDE
contig00059	1648	2847	tet(A)	0/0	100	100.0	NG_048154.1	tetracycline efflux MFS transporter Tet(A)	TETRACYCLINE

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00030	16154	17347	ACRA	0/0	100.0	99.2	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00030	12982	16131	ACRB	0/0	100.0	99.0	MEG_401	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRB	NA
contig00010	134717	137830	ACRD	0/0	100.0	98.8	MEG_407	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ACRD	NA
contig00001	501284	502441	ACRE	0/0	100.0	98.4	MEG_408	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRE	NA
contig00001	502453	505557	ACRF	0/0	100.0	97.8	MEG_409	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRF	NA
contig00001	500223	500885	ACRS	0/0	100.0	98.9	MEG_415	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS	NA
contig00009	24731	25888	AMPH	0/0	100.0	96.9	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00038	16686	17513	APH3-DPRIME	0/0	100.0	100.0	MEG_1019	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH3-DPRIME	NA
contig00038	15850	16686	APH6	0/0	100.0	100.0	MEG_1086	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH6	NA
contig00015	11035	12888	ASMA	0/0	100.0	97.8	MEG_1180	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:ASMA	NA
contig00001	300885	301704	BACA	0/0	99.8	96.7	MEG_1189	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00002	12249	12970	BAER	0/0	99.9	97.0	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00002	10849	12252	BAES	0/0	100.0	92.2	MEG_1193	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES	NA
contig00002	125467	126657	BCR	0/0	100.0	97.5	MEG_1210	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR	NA
contig00006	160327	161460	BLAEC	0/0	100.0	98.2	MEG_1278	Drugs:betalactams:Class_C_betalactamases:BLAEC	NA
contig00020	21700	22398	CPXAR	0/0	100.0	99.4	MEG_2118	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00020	22395	23768	CPXAR	0/0	100.0	98.8	MEG_2121	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00012	15391	16023	CRP	0/0	100.0	99.0	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00060	182	655	DFRA	0/0	100.0	99.8	MEG_2517	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00013	60295	61467	EMRA	0/0	100.0	98.0	MEG_2722	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA	NA
contig00013	61484	63022	EMRB	0/0	100.0	98.0	MEG_2725	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRB	NA
contig00017	87427	88617	EMRD	0/0	100.0	97.7	MEG_2729	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD	NA
contig00002	319173	320336	EMRK	0/0	100.0	98.0	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig00013	59638	60168	EMRR	0/0	100.0	99.4	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00002	317635	319173	EMRY	0/0	100.0	97.5	MEG_2736	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRY	NA
contig00006	116765	118408	EPTA	0/0	100.0	98.2	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig00002	321371	324964	EVGS	0/0	100.0	97.3	MEG_2869	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EVGS	NA
contig00029	54225	54953	GADW	0/0	100.0	97.8	MEG_3081	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig00029	55322	56146	GADX	0/0	100.0	94.3	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00005	190729	191142	HNS	0/0	100.0	99.5	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00014	7736	8413	KDPE	0/0	100.0	95.4	MEG_3448	Drugs:Aminoglycosides:Aminoglycoside_efflux_pumps:KDPE	NA
contig00023	62114	62503	MARA	0/0	100.0	99.5	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00023	61665	62099	MARR	0/0	100.0	97.9	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00008	32402	33634	MDFA	0/0	100.0	98.2	MEG_3737	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDFA	NA
contig00002	1989	3236	MDTA	0/0	100.0	96.5	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00002	3236	6358	MDTB	0/0	100.0	96.9	MEG_3747	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTB	NA
contig00002	6359	9436	MDTC	0/0	100.0	96.7	MEG_3749	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTC	NA
contig00029	49567	50724	MDTE	0/0	100.0	98.8	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00029	50749	53862	MDTF	0/0	100.0	98.5	MEG_3752	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTF	NA
contig00003	83168	84394	MDTG	0/0	100.0	98.7	MEG_3753	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig00003	73329	74537	MDTH	0/0	100.0	97.8	MEG_3755	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTH	NA
contig00011	125784	126113	MDTI	0/0	100.0	99.7	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00011	125432	125797	MDTJ	0/0	100.0	98.1	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00011	54382	55754	MDTK	0/0	99.9	98.2	MEG_3759	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:MDTK	NA
contig00007	170444	171676	MDTM	0/0	100.0	96.5	MEG_3761	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTM	NA
contig00006	93066	94097	MDTN	0/0	100.0	96.4	MEG_3763	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN	NA
contig00006	91015	93066	MDTO	0/0	100.0	96.3	MEG_3764	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTO	NA
contig00006	89552	91018	MDTP	0/0	100.0	97.5	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig00010	113536	114010	MPHB	0/0	99.6	96.6	MEG_4033	Drugs:MLS:Macrolide_phosphotransferases:MPHB	NA
contig00003	217787	219535	MSBA	0/0	100.0	99.0	MEG_4061	Drugs:Multi-drug_resistance:Multi-drug_ABC_efflux_pumps:MSBA	NA
contig00014	50257	52158	PBP2	0/0	100.0	99.0	MEG_5400	Drugs:betalactams:Penicillin_binding_protein:PBP2	NA
contig00002	382511	383815	PBP4B	0/0	100.0	96.0	MEG_5409	Drugs:betalactams:Penicillin_binding_protein:PBP4B	NA
contig00002	215066	216034	PMRF	0/0	100.0	98.1	MEG_5801	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF	NA
contig00038	5275	5931	QNRS	0/0	100.0	100.0	MEG_6020	Drugs:Fluoroquinolones:Quinolone_resistance_protein_Qnr:QNRS	NA
contig00007	118875	119744	ROBA	0/0	100.0	99.5	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00006	67586	67908	SOXS	0/0	99.7	97.5	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00038	17550	18365	SULII	0/0	100.0	100.0	MEG_6617	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULII	NA
contig00038	13902	15147	TEM	0/0	98.3	99.4	MEG_6875	Drugs:betalactams:Class_A_betalactamases:TEM	NA
contig00059	1648	2922	TETA	0/0	100.0	100.0	MEG_7024	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETA	NA
contig00015	53196	54362	UGD	0/0	100.0	97.3	MEG_7328	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:UGD	NA
contig00002	151927	153570	YOGI	0/0	100.0	97.5	MEG_7842	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:YOGI	NA

ID005

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00082	4775	5577	aph(3’’)-Ib_2	0/0	99.9	100.0	AF024602	aph(3’’)-Ib	Streptomycin
contig00082	3939	4775	aph(6)-Id_1	0/0	100.0	100.0	M28829	aph(6)-Id	Streptomycin
contig00033	39169	40044	blaCTX-M-15_1	0/0	100.0	100.0	AY044436	blaCTX-M-15	Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig00069	3905	4765	blaTEM-1B_1	0/0	100.0	100.0	AY458016	blaTEM-1B	Amoxicillin, Ampicillin, Cephalothin, Piperacillin, Ticarcillin
contig00123	153	812	catA1_1	0/0	100.0	99.5	V00622	catA1	Chloramphenicol
contig00022	6725	7198	dfrA1_8	0/0	100.0	100.0	X00926	dfrA1	Trimethoprim
contig00028	32283	33515	mdf(A)_1	0/0	100.0	98.1	Y08743	mdf(A)
contig00069	8867	9788	mph(A)_2	1/1	100.0	99.6	U36578	mph(A)	Erythromycin, Azithromycin, Spiramycin, Telithromycin
contig00097	704	1519	sul2_2	0/0	100.0	100.0	AY034138	sul2	Sulfamethoxazole
contig00111	332	1516	tet(D)_1	0/0	100.0	100.0	AF467077	tet(D)	Doxycycline, Tetracycline

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00016	12983	16132	acrB	0/0	100.0	99.0	U00096.3:484403-481253	Protein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug/proton antiporter.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00003	174089	177202	acrD	0/0	100.0	98.8	AP009048.1:2586250-2589364	AcrD is an aminoglycoside efflux pump expressed in E. coli. Its expression can be induced by indole and is regulated by baeRS and cpxAR.	aminoglycoside
contig00008	163195	164352	acrE	0/0	100.0	98.4	U00096:3413863-3415021	AcrE is a membrane fusion protein similar to AcrA.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00008	164364	167468	acrF	0/0	100.0	97.8	U00096:3415032-3418137	AcrF is a inner membrane transporter similar to AcrB.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00008	162134	162796	acrS	0/0	100.0	98.9	U00096:3413465-3412802	AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.	cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00082	4775	5578	APH(3’’)-Ib	0/0	100.0	99.9	AF313472:15593-16397	APH(3’’)-Ib is an aminoglycoside phosphotransferase encoded by plasmids transposons integrative conjugative elements and chromosomes in Enterobacteriaceae and Pseudomonas spp.	aminoglycoside
contig00082	3939	4775	APH(6)-Id	0/0	100.0	99.9	AF024602:3155-3992	APH(6)-Id is an aminoglycoside phosphotransferase encoded by plasmids integrative conjugative elements and chromosomal genomic islands in K. pneumoniae Salmonella spp. E. coli Shigella flexneri Providencia alcalifaciens Pseudomonas spp. V. cholerae Edwardsiella tarda Pasteurella multocida and Aeromonas bestiarum	aminoglycoside
contig00019	83142	83961	bacA	0/0	99.8	96.2	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00011	52912	53633	baeR	0/0	99.9	98.1	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00011	53630	55033	baeS	0/0	100.0	96.4	AP009048:2165012-2166416	BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.	aminocoumarin, aminoglycoside
contig00123	153	812	catI	0/0	100.0	99.5	V00622:243-903	catI is a chromosome and transposon-encoded variant of the cat gene found in Escherichia coli and Acinetobacter baumannii	phenicol
contig00024	22395	23768	cpxA	0/0	100.0	98.6	BA000007.3:4905062-4903688	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	aminocoumarin, aminoglycoside
contig00007	43239	43871	CRP	0/0	100.0	99.0	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00033	39169	40044	CTX-M-15	0/0	100.0	100.0	AY044436:1435-2311	CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family	cephalosporin
contig00022	6725	7198	dfrA1	0/0	100.0	99.8	KJ541681.1:19526-20000	dfrA1 is an integron-encoded dihydrofolate reductase	diaminopyrimidine
contig00012	60295	61467	emrA	0/0	100.0	98.0	AP009048:2810082-2811255	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	fluoroquinolone
contig00012	61484	63022	emrB	0/0	100.0	98.0	U00096:2812615-2814154	emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin.	fluoroquinolone
contig00018	85324	86379	emrK	0/0	100.0	97.8	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00012	59638	60168	emrR	0/0	100.0	99.4	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00018	83786	85324	emrY	0/0	100.0	97.5	D78168:1591-3130	emrY is a multidrug transport that moves substrates across the inner membrane of the Gram-negative E. coli. It is a homolog of emrB.	tetracycline
contig00005	116702	118345	eptA	0/0	100.0	98.2	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00016	16155	17348	Escherichia_coli_acrA	0/0	100.0	99.2	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00005	160265	161398	Escherichia_coli_ampC	0/0	100.0	97.7	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00003	208723	210027	Escherichia_coli_ampC1_beta-lactamase	0/0	100.0	96.0	FN649414.1:2765050-2766355	An ampC-like beta-lactamase identified from Escherichia coli.	cephalosporin, penam
contig00009	24720	25877	Escherichia_coli_ampH	0/0	100.0	96.9	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig00001	3662	3994	Escherichia_coli_emrE	0/0	100.0	98.8	Z11877.1:485-818	Member of the small MDR (multidrug resistance) family of transporters, in Escherichia coli this protein provides resistance against a number of positively charged compounds including ethidium bromide and erythromycin, proton-dependent secondary transporter which exchanges protons for compound translocation	macrolide
contig00028	32283	33515	Escherichia_coli_mdfA	0/0	100.0	96.6	JQ394987:0-1233	Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter.	benzalkonium_chloride, rhodamine, tetracycline
contig00018	86903	87517	evgA	0/0	100.0	99.0	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00018	87522	91115	evgS	0/0	100.0	96.8	U00096:2484373-2487967	EvgS is a sensor protein that phosphorylates the regulatory protein EvgA. evgS corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	fluoroquinolone, macrolide, penam, tetracycline
contig00020	56723	57451	gadW	0/0	100.0	95.6	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig00020	55530	56354	gadX	0/0	100.0	94.3	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00037	22698	23111	H-NS	0/0	100.0	99.5	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00014	7853	8530	kdpE	0/0	100.0	95.4	U00096.3:721733-721055	kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding.	aminoglycoside
contig00002	182125	182508	marA	0/0	100.0	99.5	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00011	62646	63893	mdtA	0/0	100.0	97.4	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00011	59524	62646	mdtB	0/0	100.0	96.7	U00096:2155262-2158385	MdtB is a transporter that forms a heteromultimer complex with MdtC to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex.	aminocoumarin
contig00011	56446	59523	mdtC	0/0	100.0	97.1	U00096:2158385-2161463	MdtC is a transporter that forms a heteromultimer complex with MdtB to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex. In the absence of MdtB MdtC can form a homomultimer complex that results in a functioning efflux complex with a narrower drug specificity. mdtC corresponds to 3 loci in Pseudomonas aeruginosa PAO1 (gene name: muxC/muxB) and 3 loci in Pseudomonas aeruginosa LESB58.	aminocoumarin
contig00020	60952	62109	mdtE	0/0	100.0	98.8	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00020	57814	60927	mdtF	0/0	100.0	98.5	U00096:3660413-3663527	MdtF is the multidrug inner membrane transporter for the MdtEF-TolC efflux complex.	fluoroquinolone, macrolide, penam
contig00021	72131	73357	mdtG	0/0	100.0	98.4	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00021	62292	63500	mdtH	0/0	100.0	97.8	U00096:1125326-1124117	Multidrug resistance protein MdtH	fluoroquinolone
contig00005	93066	94097	mdtN	0/0	100.0	96.4	AP009048.1:4307588-4306556	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	acridine_dye, nucleoside
contig00005	91015	93066	mdtO	0/0	100.0	96.3	AP009048.1:4306557-4304505	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00005	89552	91018	mdtP	0/0	100.0	97.5	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00069	8883	9788	mphA	0/0	100.0	99.9	D16251.1:2531-1625	The mphA gene encodes for resistance enzyme MPH(2’)-I which preferentially inactivate 14-membered macrolides (e.g.erythromycin telithromycin roxithromycin) over 16-membered macrolides (e.g.tylosin spiramycin). It phosphorylates macrolides at 2’-OH hydroxyl of desosamine sugar of macrolides in a GTP-dependent manner.	macrolide
contig00003	152908	153382	mphB	0/0	99.6	96.6	AE005174.2:3397370-3397847	The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides.	macrolide
contig00006	140147	141895	msbA	0/0	100.0	99.0	U00096.3:966620-968369	MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability.	nitroimidazole
contig00026	63223	64191	pmrF	0/0	100.0	98.1	U00096:2367070-2368039	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide
contig00022	6106	6630	SAT-1	0/0	100.0	100.0	AB211124:0-525	SAT-2 is a plasmid-mediated streptothricin acetyltransferase which confers resistance to streptothricin a nucleoside antibiotic. Originally described from an E. coli plasmid sequence by Heim et al. 1989.	nucleoside
contig00097	704	1519	sul2	0/0	100.0	100.0	AY055428.1:21084-20268	Sul2 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria usually found on small plasmids.	sulfonamide
contig00069	3905	4765	TEM-1	0/0	100.0	99.9	AL513383:161910-162771	TEM-1 is a broad-spectrum beta-lactamase found in many Gram-negative bacteria. Confers resistance to penicillins and first generation cephalosphorins.	cephalosporin, monobactam, penam, penem
contig00111	332	1516	tet(D)	0/0	100.0	100.0	AF467077.1:163-1348	TetD is a tetracycline efflux pump found exclusively in Gram-negative bacteria.	tetracycline
contig00019	60943	62430	tolC	0/0	100.0	98.5	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan
contig00011	120102	121268	ugd	0/0	100.0	97.5	U00096:2099613-2098446	PmrE is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin	peptide
contig00026	84	1727	yojI	0/0	100.0	97.5	U00096.3:2308615-2306971	YojI mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. YojI is capable of pumping out microcin molecules. The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI.	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00022	5260	6059	(AGly)aadA1-pm	1/3	96.3	99.5	JQ690540:7968-8798	(AGly)aadA1-pm	NA
contig00022	6106	6630	(AGly)sat-2A	0/0	100.0	100.0	X51546:518-1042	(AGly)sat-2A	NA
contig00082	4775	5578	(AGly)strA	0/0	100.0	100.0	AB366441:22458-23261	(AGly)strA	NA
contig00082	3939	4775	(AGly)strB	0/0	100.0	100.0	FJ474091:264-1100	(AGly)strB	NA
contig00003	208723	210027	(Bla)AmpC1_Ecoli	0/0	100.0	96.0	FN649414:2765051-2766355	(Bla)AmpC1_Ecoli	NA
contig00005	160265	161398	(Bla)AmpC2_Ecoli	0/0	100.0	97.7	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00009	24720	25877	(Bla)ampH_Ecoli	0/0	100.0	96.9	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00033	39169	40044	(Bla)blaCTX-M-15	0/0	100.0	100.0	JQ686199:261-1136	(Bla)blaCTX-M-15	NA
contig00069	3905	4765	(Bla)blaTEM-105	0/0	100.0	99.9	AF516720:215-1075	(Bla)blaTEM-105	NA
contig00014	50375	52276	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100.0	99.0	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA
contig00069	8883	9788	(MLS)mph(A)	0/0	100.0	99.9	DQ445270:1626-2531	(MLS)mph(A)	NA
contig00123	153	812	(Phe)catA1	0/0	100.0	99.5	V00622:244-903	(Phe)catA1	NA
contig00097	704	1519	(Sul)sul2	0/0	100.0	100.0	EU360945:1617-2432	(Sul)sul2	NA
contig00111	332	1516	(Tet)tetD	0/0	100.0	100.0	AB089602:1521-2705	(Tet)tetD	NA
contig00022	6725	7198	(Tmt)dfrA1	0/0	100.0	100.0	JQ794607:474	(Tmt)dfrA1	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00022	5260	6048	aadA1	0/0	100	100.0	NG_047327.1	ANT(3’’)-Ia family aminoglycoside nucleotidyltransferase AadA1	STREPTOMYCIN
contig00082	4775	5602	aph(3’’)-Ib	0/0	100	99.9	NG_056002.2	aminoglycoside O-phosphotransferase APH(3’’)-Ib	STREPTOMYCIN
contig00082	3939	4775	aph(6)-Id	0/0	100	100.0	NG_047464.1	aminoglycoside O-phosphotransferase APH(6)-Id	STREPTOMYCIN
contig00033	39169	40044	blaCTX-M-15	0/0	100	100.0	NG_048935.1	class A extended-spectrum beta-lactamase CTX-M-15	CEPHALOSPORIN
contig00005	160265	161398	blaEC-8	0/0	100	98.2	NG_049086.1	cephalosporin-hydrolyzing class C beta-lactamase EC-8	CEPHALOSPORIN
contig00069	3905	4765	blaTEM-1	0/0	100	100.0	NG_050145.1	class A broad-spectrum beta-lactamase TEM-1	BETA-LACTAM
contig00123	153	812	catA1	0/0	100	100.0	NG_047586.1	type A-1 chloramphenicol O-acetyltransferase	CHLORAMPHENICOL
contig00022	6725	7198	dfrA1	0/0	100	100.0	NG_047676.1	trimethoprim-resistant dihydrofolate reductase DfrA1	TRIMETHOPRIM
contig00069	8867	9788	mph(A)	1/1	100	99.6	NG_047986.1	Mph(A) family macrolide 2’-phosphotransferase	MACROLIDE
contig00022	6106	6630	sat2_gen	0/0	100	100.0	NG_048068.1	streptothricin N-acetyltransferase Sat2	STREPTOTHRICIN
contig00097	704	1519	sul2	0/0	100	100.0	NG_051852.1	sulfonamide-resistant dihydropteroate synthase Sul2	SULFONAMIDE
contig00111	332	1516	tet(D)	0/0	100	99.9	NG_048184.1	tetracycline efflux MFS transporter Tet(D)	TETRACYCLINE

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00016	16155	17348	ACRA	0/0	100.0	99.2	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00016	12983	16132	ACRB	0/0	100.0	99.0	MEG_401	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRB	NA
contig00003	174089	177202	ACRD	0/0	100.0	98.8	MEG_407	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ACRD	NA
contig00008	163195	164352	ACRE	0/0	100.0	98.4	MEG_408	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRE	NA
contig00008	164364	167468	ACRF	0/0	100.0	97.8	MEG_409	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRF	NA
contig00008	162134	162796	ACRS	0/0	100.0	98.9	MEG_415	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS	NA
contig00009	24720	25877	AMPH	0/0	100.0	96.9	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00022	5260	6059	ANT3-DPRIME	1/3	96.3	99.5	MEG_915	Drugs:Aminoglycosides:Aminoglycoside_O-nucleotidyltransferases:ANT3-DPRIME	NA
contig00082	4775	5602	APH3-DPRIME	0/0	100.0	99.9	MEG_1019	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH3-DPRIME	NA
contig00082	3939	4775	APH6	0/0	100.0	100.0	MEG_1086	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH6	NA
contig00011	75828	77680	ASMA	0/0	100.0	98.3	MEG_1180	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:ASMA	NA
contig00019	83142	83961	BACA	0/0	99.8	96.7	MEG_1189	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00011	52912	53633	BAER	0/0	99.9	98.1	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00011	53630	55033	BAES	0/0	100.0	96.4	MEG_1193	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES	NA
contig00032	19024	20214	BCR	0/0	100.0	97.5	MEG_1210	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR	NA
contig00005	160265	161398	BLAEC	0/0	100.0	98.2	MEG_1278	Drugs:betalactams:Class_C_betalactamases:BLAEC	NA
contig00123	142	812	CATA	0/0	100.0	99.7	MEG_1593	Drugs:Phenicol:Chloramphenicol_acetyltransferases:CATA	NA
contig00024	21700	22398	CPXAR	0/0	100.0	99.4	MEG_2118	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00024	22395	23768	CPXAR	0/0	100.0	98.8	MEG_2121	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00007	43239	43871	CRP	0/0	100.0	99.0	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00022	6725	7198	DFRA	0/0	100.0	99.8	MEG_2495	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00012	60295	61467	EMRA	0/0	100.0	98.0	MEG_2722	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA	NA
contig00012	61484	63022	EMRB	0/0	100.0	98.0	MEG_2725	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRB	NA
contig00022	67069	68259	EMRD	0/0	100.0	97.7	MEG_2729	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD	NA
contig00018	85324	86487	EMRK	0/0	100.0	98.0	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig00012	59638	60168	EMRR	0/0	100.0	99.4	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00018	83786	85324	EMRY	0/0	100.0	97.5	MEG_2736	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRY	NA
contig00005	116702	118345	EPTA	0/0	100.0	98.2	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig00018	87522	91115	EVGS	0/0	100.0	97.3	MEG_2869	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EVGS	NA
contig00020	56723	57451	GADW	0/0	100.0	97.8	MEG_3081	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig00020	55530	56354	GADX	0/0	100.0	94.3	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00037	22698	23111	HNS	0/0	100.0	99.5	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00014	7853	8530	KDPE	0/0	100.0	95.4	MEG_3448	Drugs:Aminoglycosides:Aminoglycoside_efflux_pumps:KDPE	NA
contig00002	182125	182514	MARA	0/0	100.0	99.5	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00002	182529	182963	MARR	0/0	100.0	97.9	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00028	32283	33515	MDFA	0/0	100.0	98.2	MEG_3737	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDFA	NA
contig00011	62646	63893	MDTA	0/0	100.0	97.4	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00011	59524	62646	MDTB	0/0	100.0	96.7	MEG_3747	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTB	NA
contig00011	56446	59523	MDTC	0/0	100.0	97.1	MEG_3749	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTC	NA
contig00020	60952	62109	MDTE	0/0	100.0	98.8	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00020	57814	60927	MDTF	0/0	100.0	98.5	MEG_3752	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTF	NA
contig00021	72131	73357	MDTG	0/0	100.0	98.6	MEG_3753	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig00021	62292	63500	MDTH	0/0	100.0	97.8	MEG_3755	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTH	NA
contig00002	143629	143958	MDTI	0/0	100.0	99.7	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00002	143277	143642	MDTJ	0/0	100.0	98.1	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00002	72227	73599	MDTK	0/0	99.9	98.2	MEG_3759	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:MDTK	NA
contig00005	93066	94097	MDTN	0/0	100.0	96.4	MEG_3763	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN	NA
contig00005	91015	93066	MDTO	0/0	100.0	96.3	MEG_3764	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTO	NA
contig00005	89552	91018	MDTP	0/0	100.0	97.5	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig00069	8867	9788	MPHA	1/1	100.0	99.6	MEG_4030	Drugs:MLS:Macrolide_phosphotransferases:MPHA	NA
contig00003	152908	153382	MPHB	0/0	99.6	96.6	MEG_4033	Drugs:MLS:Macrolide_phosphotransferases:MPHB	NA
contig00006	140147	141895	MSBA	0/0	100.0	99.0	MEG_4061	Drugs:Multi-drug_resistance:Multi-drug_ABC_efflux_pumps:MSBA	NA
contig00001	3662	3994	MVRC	0/0	100.0	98.8	MEG_4103	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MVRC	NA
contig00014	50375	52276	PBP2	0/0	100.0	99.0	MEG_5400	Drugs:betalactams:Penicillin_binding_protein:PBP2	NA
contig00003	208723	210027	PBP4B	0/0	100.0	96.0	MEG_5409	Drugs:betalactams:Penicillin_binding_protein:PBP4B	NA
contig00026	63223	64191	PMRF	0/0	100.0	98.1	MEG_5801	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF	NA
contig00013	60761	61630	ROBA	0/0	100.0	99.5	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00005	67586	67908	SOXS	0/0	99.7	97.5	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00097	704	1519	SULII	0/0	100.0	100.0	MEG_6617	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULII	NA
contig00069	3887	5132	TEM	0/0	98.3	99.4	MEG_6875	Drugs:betalactams:Class_A_betalactamases:TEM	NA
contig00111	332	1516	TETC	0/0	100.0	99.9	MEG_7061	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETC	NA
contig00011	120102	121268	UGD	0/0	100.0	97.5	MEG_7328	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:UGD	NA
contig00026	84	1727	YOGI	0/0	100.0	97.5	MEG_7842	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:YOGI	NA

ID006

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00087	9348	10184	aph(6)-Id_1	0/0	100	100.0	M28829	aph(6)-Id	Streptomycin
contig00117	1703	2578	blaCTX-M-15_1	0/0	100	100.0	AY044436	blaCTX-M-15	Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig00097	3904	4764	blaTEM-1B_1	0/0	100	100.0	AY458016	blaTEM-1B	Amoxicillin, Ampicillin, Cephalothin, Piperacillin, Ticarcillin
contig00125	182	664	dfrA14_5	0/0	100	99.6	DQ388123	dfrA14	Trimethoprim
contig00003	28294	29526	mdf(A)_1	0/0	100	99.4	Y08743	mdf(A)
contig00091	5805	6461	qnrS1_1	0/0	100	100.0	AB187515	qnrS1	Ciprofloxacin
contig00118	264	1079	sul2_2	0/0	100	100.0	AY034138	sul2	Sulfamethoxazole

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00017	3291	6440	acrB	0/0	100.0	99.9	U00096.3:484403-481253	Protein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug/proton antiporter.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00001	135224	138337	acrD	0/0	100.0	99.2	AP009048.1:2586250-2589364	AcrD is an aminoglycoside efflux pump expressed in E. coli. Its expression can be induced by indole and is regulated by baeRS and cpxAR.	aminoglycoside
contig00046	8610	9767	acrE	0/0	100.0	99.0	U00096:3413863-3415021	AcrE is a membrane fusion protein similar to AcrA.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00046	5494	8598	acrF	0/0	100.0	99.0	U00096:3415032-3418137	AcrF is a inner membrane transporter similar to AcrB.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00046	10166	10828	acrS	0/0	100.0	99.1	U00096:3413465-3412802	AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.	cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00087	9348	10184	APH(6)-Id	0/0	100.0	99.9	AF024602:3155-3992	APH(6)-Id is an aminoglycoside phosphotransferase encoded by plasmids integrative conjugative elements and chromosomal genomic islands in K. pneumoniae Salmonella spp. E. coli Shigella flexneri Providencia alcalifaciens Pseudomonas spp. V. cholerae Edwardsiella tarda Pasteurella multocida and Aeromonas bestiarum	aminoglycoside
contig00024	45230	46051	bacA	0/0	100.0	100.0	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00038	30484	31206	baeR	0/0	100.0	100.0	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00038	31203	32606	baeS	0/0	100.0	99.9	AP009048:2165012-2166416	BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.	aminocoumarin, aminoglycoside
contig00026	40358	41731	cpxA	0/0	100.0	98.8	BA000007.3:4905062-4903688	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	aminocoumarin, aminoglycoside
contig00008	9683	10315	CRP	0/0	100.0	99.4	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00117	1703	2578	CTX-M-15	0/0	100.0	100.0	AY044436:1435-2311	CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family	cephalosporin
contig00125	182	664	dfrA14	0/0	100.0	99.8	EU780012:2162-2645	dfrA14 is an integron-encoded dihydrofolate reductase found in Escherichia coli	diaminopyrimidine
contig00011	22835	24007	emrA	0/0	100.0	99.8	AP009048:2810082-2811255	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	fluoroquinolone
contig00011	24024	25562	emrB	0/0	100.0	99.9	U00096:2812615-2814154	emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin.	fluoroquinolone
contig00016	51283	52338	emrK	0/0	100.0	100.0	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00011	22178	22708	emrR	0/0	100.0	100.0	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00016	49745	51283	emrY	0/0	100.0	99.9	D78168:1591-3130	emrY is a multidrug transport that moves substrates across the inner membrane of the Gram-negative E. coli. It is a homolog of emrB.	tetracycline
contig00028	18487	20130	eptA	0/0	100.0	99.8	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00017	6463	7656	Escherichia_coli_acrA	0/0	100.0	100.0	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00028	62348	63481	Escherichia_coli_ampC	0/0	100.0	97.2	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00001	180080	181384	Escherichia_coli_ampC1_beta-lactamase	0/0	100.0	99.2	FN649414.1:2765050-2766355	An ampC-like beta-lactamase identified from Escherichia coli.	cephalosporin, penam
contig00066	15777	16934	Escherichia_coli_ampH	0/0	100.0	98.9	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig00002	132610	132942	Escherichia_coli_emrE	0/0	100.0	91.9	Z11877.1:485-818	Member of the small MDR (multidrug resistance) family of transporters, in Escherichia coli this protein provides resistance against a number of positively charged compounds including ethidium bromide and erythromycin, proton-dependent secondary transporter which exchanges protons for compound translocation	macrolide
contig00003	28294	29526	Escherichia_coli_mdfA	0/0	100.0	97.9	JQ394987:0-1233	Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter.	benzalkonium_chloride, rhodamine, tetracycline
contig00016	52862	53476	evgA	0/0	100.0	100.0	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00016	53481	57074	evgS	0/0	100.0	100.0	U00096:2484373-2487967	EvgS is a sensor protein that phosphorylates the regulatory protein EvgA. evgS corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	fluoroquinolone, macrolide, penam, tetracycline
contig00075	4569	5297	gadW	0/0	100.0	94.7	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig00075	3377	4201	gadX	0/0	100.0	99.9	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00004	147963	148376	H-NS	0/0	100.0	99.3	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00013	8269	8946	kdpE	0/0	100.0	100.0	U00096.3:721733-721055	kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding.	aminoglycoside
contig00015	34204	34587	marA	0/0	100.0	100.0	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00038	40219	41466	mdtA	0/0	100.0	97.2	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00038	37097	40219	mdtB	0/0	100.0	99.5	U00096:2155262-2158385	MdtB is a transporter that forms a heteromultimer complex with MdtC to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex.	aminocoumarin
contig00038	34019	37096	mdtC	0/0	100.0	99.8	U00096:2158385-2161463	MdtC is a transporter that forms a heteromultimer complex with MdtB to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex. In the absence of MdtB MdtC can form a homomultimer complex that results in a functioning efflux complex with a narrower drug specificity. mdtC corresponds to 3 loci in Pseudomonas aeruginosa PAO1 (gene name: muxC/muxB) and 3 loci in Pseudomonas aeruginosa LESB58.	aminocoumarin
contig00075	8798	9955	mdtE	0/0	100.0	100.0	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00075	5660	8773	mdtF	0/0	100.0	100.0	U00096:3660413-3663527	MdtF is the multidrug inner membrane transporter for the MdtEF-TolC efflux complex.	fluoroquinolone, macrolide, penam
contig00019	68680	69906	mdtG	0/0	100.0	99.7	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00019	58841	60049	mdtH	0/0	100.0	98.4	U00096:1125326-1124117	Multidrug resistance protein MdtH	fluoroquinolone
contig00037	38798	40030	mdtM	0/0	100.0	95.0	U00096.3:4568519-4567286	Multidrug resistance protein MdtM	acridine_dye, fluoroquinolone, lincosamide, nucleoside, phenicol
contig00042	26401	27432	mdtN	0/0	100.0	100.0	AP009048.1:4307588-4306556	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	acridine_dye, nucleoside
contig00042	24350	26401	mdtO	0/0	100.0	99.1	AP009048.1:4306557-4304505	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00042	22887	24353	mdtP	0/0	100.0	100.0	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00001	114017	114491	mphB	0/0	99.6	97.0	AE005174.2:3397370-3397847	The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides.	macrolide
contig00005	51413	53161	msbA	0/0	100.0	100.0	U00096.3:966620-968369	MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability.	nitroimidazole
contig00010	34451	35419	pmrF	0/0	100.0	100.0	U00096:2367070-2368039	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide
contig00091	5805	6461	QnrS1	0/0	100.0	100.0	DQ485529.1:0-657	QnrS1 is a plasmid-mediated quinolone resistance protein found in Shigella flexneri	fluoroquinolone
contig00118	264	1079	sul2	0/0	100.0	100.0	AY055428.1:21084-20268	Sul2 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria usually found on small plasmids.	sulfonamide
contig00097	3904	4764	TEM-1	0/0	100.0	99.9	AL513383:161910-162771	TEM-1 is a broad-spectrum beta-lactamase found in many Gram-negative bacteria. Confers resistance to penicillins and first generation cephalosphorins.	cephalosporin, monobactam, penam, penem
contig00024	68426	69913	tolC	0/0	100.0	99.7	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan
contig00010	93683	95326	yojI	0/0	100.0	99.8	U00096.3:2308615-2306971	YojI mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. YojI is capable of pumping out microcin molecules. The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI.	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00087	9348	10184	(AGly)strB	0/0	100	100.0	FJ474091:264-1100	(AGly)strB	NA
contig00001	180080	181384	(Bla)AmpC1_Ecoli	0/0	100	99.2	FN649414:2765051-2766355	(Bla)AmpC1_Ecoli	NA
contig00028	62348	63481	(Bla)AmpC2_Ecoli	0/0	100	97.2	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00066	15777	16934	(Bla)ampH_Ecoli	0/0	100	98.9	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00117	1703	2578	(Bla)blaCTX-M-15	0/0	100	100.0	JQ686199:261-1136	(Bla)blaCTX-M-15	NA
contig00097	3904	4764	(Bla)blaTEM-105	0/0	100	99.9	AF516720:215-1075	(Bla)blaTEM-105	NA
contig00013	54775	56676	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100	99.4	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA
contig00091	5805	6461	(Flq)qnr-S1	0/0	100	100.0	AB187515:9737-10393	(Flq)qnr-S1	NA
contig00118	264	1079	(Sul)sul2	0/0	100	100.0	EU360945:1617-2432	(Sul)sul2	NA
contig00097	4937	5587	(Tet)tetR	0/0	100	100.0	HF545434:53576-54226	(Tet)tetR	NA
contig00125	182	655	(Tmt)dfrA14	0/0	100	100.0	GU726917:72-545	(Tmt)dfrA14	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00087	9348	10184	aph(6)-Id	0/0	100	100.0	NG_047464.1	aminoglycoside O-phosphotransferase APH(6)-Id	STREPTOMYCIN
contig00117	1703	2578	blaCTX-M-15	0/0	100	100.0	NG_048935.1	class A extended-spectrum beta-lactamase CTX-M-15	CEPHALOSPORIN
contig00028	62348	63481	blaEC-15	0/0	100	98.4	NG_049081.1	class C extended-spectrum beta-lactamase EC-15	CEPHALOSPORIN
contig00097	3904	4764	blaTEM-1	0/0	100	100.0	NG_050145.1	class A broad-spectrum beta-lactamase TEM-1	BETA-LACTAM
contig00125	182	655	dfrA14	0/0	100	100.0	NG_056035.1	trimethoprim-resistant dihydrofolate reductase DfrA14	TRIMETHOPRIM
contig00091	5805	6461	qnrS1	0/0	100	100.0	NG_050543.1	quinolone resistance pentapeptide repeat protein QnrS1	QUINOLONE
contig00118	264	1079	sul2	0/0	100	100.0	NG_051852.1	sulfonamide-resistant dihydropteroate synthase Sul2	SULFONAMIDE

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00017	6463	7656	ACRA	0/0	100.0	100.0	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00017	3291	6440	ACRB	0/0	100.0	99.9	MEG_401	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRB	NA
contig00001	135224	138337	ACRD	0/0	100.0	99.2	MEG_407	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ACRD	NA
contig00046	8610	9767	ACRE	0/0	100.0	99.0	MEG_408	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRE	NA
contig00046	5494	8598	ACRF	0/0	100.0	99.0	MEG_409	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRF	NA
contig00046	10166	10828	ACRS	0/0	100.0	99.1	MEG_415	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS	NA
contig00066	15777	16934	AMPH	0/0	100.0	98.9	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00087	9348	10184	APH6	0/0	100.0	100.0	MEG_1086	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH6	NA
contig00012	11912	13764	ASMA	0/0	100.0	98.4	MEG_1180	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:ASMA	NA
contig00024	45230	46051	BACA	0/0	100.0	100.0	MEG_1190	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00038	30484	31206	BAER	0/0	100.0	100.0	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00038	31203	32606	BAES	0/0	100.0	99.9	MEG_1193	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES	NA
contig00025	48855	50045	BCR	0/0	100.0	100.0	MEG_1210	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR	NA
contig00028	62348	63481	BLAEC	0/0	100.0	98.4	MEG_1282	Drugs:betalactams:Class_C_betalactamases:BLAEC	NA
contig00026	39663	40361	CPXAR	0/0	100.0	99.9	MEG_2118	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00026	40358	41731	CPXAR	0/0	100.0	99.5	MEG_2121	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00008	9683	10315	CRP	0/0	100.0	99.4	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00125	182	655	DFRA	0/0	100.0	99.8	MEG_2517	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00011	22835	24007	EMRA	0/0	100.0	99.8	MEG_2722	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA	NA
contig00011	24024	25562	EMRB	0/0	100.0	99.9	MEG_2725	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRB	NA
contig00020	75717	76907	EMRD	0/0	100.0	99.8	MEG_2729	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD	NA
contig00016	51283	52446	EMRK	0/0	100.0	100.0	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig00011	22178	22708	EMRR	0/0	100.0	100.0	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00016	49745	51283	EMRY	0/0	100.0	100.0	MEG_2736	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRY	NA
contig00028	18487	20130	EPTA	0/0	100.0	99.8	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig00016	53481	57074	EVGS	0/0	100.0	100.0	MEG_2870	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EVGS	NA
contig00075	4569	5297	GADW	0/0	100.0	100.0	MEG_3081	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig00075	3377	4201	GADX	0/0	100.0	99.9	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00004	147963	148376	HNS	0/0	100.0	99.3	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00013	8269	8946	KDPE	0/0	100.0	100.0	MEG_3448	Drugs:Aminoglycosides:Aminoglycoside_efflux_pumps:KDPE	NA
contig00015	34198	34587	MARA	0/0	100.0	100.0	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00015	33750	34184	MARR	0/0	100.0	97.5	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00003	28294	29526	MDFA	0/0	100.0	99.5	MEG_3737	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDFA	NA
contig00038	40219	41466	MDTA	0/0	100.0	97.2	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00038	37097	40219	MDTB	0/0	100.0	99.5	MEG_3747	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTB	NA
contig00038	34019	37096	MDTC	0/0	100.0	99.8	MEG_3749	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTC	NA
contig00075	8798	9955	MDTE	0/0	100.0	100.0	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00075	5660	8773	MDTF	0/0	100.0	100.0	MEG_3752	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTF	NA
contig00019	68680	69906	MDTG	0/0	100.0	99.7	MEG_3754	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig00019	58841	60049	MDTH	0/0	100.0	98.4	MEG_3755	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTH	NA
contig00007	15413	15742	MDTI	0/0	100.0	100.0	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00007	15729	16094	MDTJ	0/0	100.0	99.5	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00007	85852	87225	MDTK	0/0	100.0	98.9	MEG_3759	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:MDTK	NA
contig00037	38798	40030	MDTM	0/0	100.0	95.0	MEG_3761	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTM	NA
contig00042	26401	27432	MDTN	0/0	100.0	100.0	MEG_3763	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN	NA
contig00042	24350	26401	MDTO	0/0	100.0	99.1	MEG_3764	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTO	NA
contig00042	22887	24353	MDTP	0/0	100.0	100.0	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig00001	114017	114491	MPHB	0/0	99.6	97.0	MEG_4033	Drugs:MLS:Macrolide_phosphotransferases:MPHB	NA
contig00005	51413	53161	MSBA	0/0	100.0	100.0	MEG_4061	Drugs:Multi-drug_resistance:Multi-drug_ABC_efflux_pumps:MSBA	NA
contig00002	132610	132942	MVRC	0/0	100.0	91.9	MEG_4103	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MVRC	NA
contig00013	54775	56676	PBP2	0/0	100.0	99.4	MEG_5400	Drugs:betalactams:Penicillin_binding_protein:PBP2	NA
contig00001	180080	181384	PBP4B	0/0	100.0	99.2	MEG_5409	Drugs:betalactams:Penicillin_binding_protein:PBP4B	NA
contig00010	34451	35419	PMRF	0/0	100.0	100.0	MEG_5801	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF	NA
contig00091	5805	6461	QNRS	0/0	100.0	100.0	MEG_6020	Drugs:Fluoroquinolones:Quinolone_resistance_protein_Qnr:QNRS	NA
contig00039	19099	19968	ROBA	0/0	100.0	100.0	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00042	720	1043	SOXS	0/0	100.0	100.0	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00118	264	1079	SULII	0/0	100.0	100.0	MEG_6617	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULII	NA
contig00097	3537	4782	TEM	0/0	98.3	99.4	MEG_6875	Drugs:betalactams:Class_A_betalactamases:TEM	NA
contig00010	93683	95326	YOGI	0/0	100.0	99.8	MEG_7842	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:YOGI	NA

ID007I

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00087	1505	2293	aadA5_1	0/0	100.0	100.0	AF137361	aadA5	Streptomycin
contig00107	887	1690	aph(3’’)-Ib_5	0/0	100.0	100.0	AF321551	aph(3’’)-Ib	Streptomycin
contig00107	51	887	aph(6)-Id_1	0/0	100.0	99.9	M28829	aph(6)-Id	Streptomycin
contig00142	247	1122	blaCTX-M-27_1	0/0	100.0	100.0	AY156923	blaCTX-M-27	Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig00071	10414	11274	blaTEM-1B_1	0/0	100.0	100.0	AY458016	blaTEM-1B	Amoxicillin, Ampicillin, Cephalothin, Piperacillin, Ticarcillin
contig00087	901	1374	dfrA17_1	0/0	100.0	100.0	FJ460238	dfrA17	Trimethoprim
contig00012	29918	31150	mdf(A)_1	0/0	100.0	97.8	Y08743	mdf(A)
contig00087	2813	3679	sul1_5	0/0	100.0	99.9	EU780013	sul1	Sulfamethoxazole
contig00107	1751	2566	sul2_2	0/0	100.0	100.0	AY034138	sul2	Sulfamethoxazole
contig00121	633	1879	tet(A)_6	0/0	97.8	100.0	AF534183	tet(A)	Doxycycline, Tetracycline

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00087	1505	2293	aadA5	0/0	100.0	100.0	AF137361:63-852	aadA5 is an aminoglycoside nucleotidyltransferase gene encoded by plasmids transposons and integrons in E. coli K. pneumoniae Kluyvera georgiana P. aeruginosa and E. cloacae	aminoglycoside
contig00010	137241	140390	acrB	0/0	100.0	98.8	U00096.3:484403-481253	Protein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug/proton antiporter.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00006	127119	130232	acrD	0/0	100.0	98.7	AP009048.1:2586250-2589364	AcrD is an aminoglycoside efflux pump expressed in E. coli. Its expression can be induced by indole and is regulated by baeRS and cpxAR.	aminoglycoside
contig00008	149305	150462	acrE	0/0	100.0	98.8	U00096:3413863-3415021	AcrE is a membrane fusion protein similar to AcrA.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00008	150474	153578	acrF	0/0	100.0	96.6	U00096:3415032-3418137	AcrF is a inner membrane transporter similar to AcrB.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00008	148244	148906	acrS	0/0	100.0	98.3	U00096:3413465-3412802	AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.	cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00107	887	1690	APH(3’’)-Ib	0/0	100.0	99.8	AF313472:15593-16397	APH(3’’)-Ib is an aminoglycoside phosphotransferase encoded by plasmids transposons integrative conjugative elements and chromosomes in Enterobacteriaceae and Pseudomonas spp.	aminoglycoside
contig00107	51	887	APH(6)-Id	0/0	100.0	99.8	AF024602:3155-3992	APH(6)-Id is an aminoglycoside phosphotransferase encoded by plasmids integrative conjugative elements and chromosomal genomic islands in K. pneumoniae Salmonella spp. E. coli Shigella flexneri Providencia alcalifaciens Pseudomonas spp. V. cholerae Edwardsiella tarda Pasteurella multocida and Aeromonas bestiarum	aminoglycoside
contig00009	129450	130269	bacA	0/0	99.8	98.3	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00002	166453	167174	baeR	0/0	99.9	97.1	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00002	167171	168574	baeS	0/0	100.0	90.5	AP009048:2165012-2166416	BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.	aminocoumarin, aminoglycoside
contig00013	66690	68057	cpxA	0/0	99.6	98.5	BA000007.3:4905062-4903688	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	aminocoumarin, aminoglycoside
contig00007	15089	15721	CRP	0/0	100.0	99.2	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00142	247	1122	CTX-M-27	0/0	100.0	100.0	AY156923:0-876	CTX-M-27 is a beta-lactamase found in Escherichia coli	cephalosporin
contig00087	901	1374	dfrA17	0/0	100.0	100.0	DQ838665:0-474	dfrA17 is an integron-encoded dihydrofolate reductase found in Escherichia coli	diaminopyrimidine
contig00005	47612	48784	emrA	0/0	100.0	98.0	AP009048:2810082-2811255	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	fluoroquinolone
contig00005	48801	50339	emrB	0/0	100.0	98.4	U00096:2812615-2814154	emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin.	fluoroquinolone
contig00078	5717	6772	emrK	0/0	100.0	97.7	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00005	46955	47485	emrR	0/0	100.0	98.5	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00078	4179	5717	emrY	0/0	100.0	97.7	D78168:1591-3130	emrY is a multidrug transport that moves substrates across the inner membrane of the Gram-negative E. coli. It is a homolog of emrB.	tetracycline
contig00033	17540	19183	eptA	0/0	100.0	91.4	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00010	140413	141606	Escherichia_coli_acrA	0/0	100.0	99.1	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00037	13287	14420	Escherichia_coli_ampC	0/0	100.0	97.8	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00010	51334	52491	Escherichia_coli_ampH	0/0	100.0	97.1	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig00019	28735	29067	Escherichia_coli_emrE	0/0	100.0	92.2	Z11877.1:485-818	Member of the small MDR (multidrug resistance) family of transporters, in Escherichia coli this protein provides resistance against a number of positively charged compounds including ethidium bromide and erythromycin, proton-dependent secondary transporter which exchanges protons for compound translocation	macrolide
contig00012	29918	31150	Escherichia_coli_mdfA	0/0	100.0	96.3	JQ394987:0-1233	Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter.	benzalkonium_chloride, rhodamine, tetracycline
contig00078	7296	7910	evgA	0/0	100.0	99.0	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00058	1556	2284	gadW	0/0	100.0	100.0	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig00058	363	1187	gadX	0/0	100.0	93.9	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00026	22379	22792	H-NS	0/0	100.0	99.3	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00017	3031	3703	kdpE	0/0	99.3	95.5	U00096.3:721733-721055	kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding.	aminoglycoside
contig00001	221588	221971	marA	0/0	100.0	99.0	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00002	176187	177434	mdtA	0/0	100.0	95.6	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00002	173065	176187	mdtB	0/0	100.0	96.2	U00096:2155262-2158385	MdtB is a transporter that forms a heteromultimer complex with MdtC to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex.	aminocoumarin
contig00002	169987	173064	mdtC	0/0	100.0	94.0	U00096:2158385-2161463	MdtC is a transporter that forms a heteromultimer complex with MdtB to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex. In the absence of MdtB MdtC can form a homomultimer complex that results in a functioning efflux complex with a narrower drug specificity. mdtC corresponds to 3 loci in Pseudomonas aeruginosa PAO1 (gene name: muxC/muxB) and 3 loci in Pseudomonas aeruginosa LESB58.	aminocoumarin
contig00058	5785	6942	mdtE	0/0	100.0	98.5	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00058	2647	5760	mdtF	0/0	100.0	97.3	U00096:3660413-3663527	MdtF is the multidrug inner membrane transporter for the MdtEF-TolC efflux complex.	fluoroquinolone, macrolide, penam
contig00016	91892	93118	mdtG	0/0	100.0	98.4	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00016	82055	83263	mdtH	0/0	100.0	98.3	U00096:1125326-1124117	Multidrug resistance protein MdtH	fluoroquinolone
contig00023	81590	82822	mdtM	0/0	100.0	95.0	U00096.3:4568519-4567286	Multidrug resistance protein MdtM	acridine_dye, fluoroquinolone, lincosamide, nucleoside, phenicol
contig00052	12253	13284	mdtN	0/0	100.0	96.2	AP009048.1:4307588-4306556	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	acridine_dye, nucleoside
contig00052	10202	12253	mdtO	0/0	100.0	97.1	AP009048.1:4306557-4304505	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00052	8739	10205	mdtP	0/0	100.0	97.6	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00004	103917	105665	msbA	0/0	100.0	98.1	U00096.3:966620-968369	MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability.	nitroimidazole
contig00027	10123	11091	pmrF	0/0	100.0	97.6	U00096:2367070-2368039	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide
contig00087	2840	3679	sul1	0/0	100.0	100.0	JF969163:1053-1893	Sul1 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria. It is linked to other resistance genes of class 1 integrons.	sulfonamide
contig00107	1751	2566	sul2	0/0	100.0	100.0	AY055428.1:21084-20268	Sul2 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria usually found on small plasmids.	sulfonamide
contig00071	10414	11274	TEM-1	0/0	100.0	99.9	AL513383:161910-162771	TEM-1 is a broad-spectrum beta-lactamase found in many Gram-negative bacteria. Confers resistance to penicillins and first generation cephalosphorins.	cephalosporin, monobactam, penam, penem
contig00121	633	1879	tet(A)	0/0	97.8	100.0	AF534183.1:2970-4245	TetA is a tetracycline efflux pump found in many species of Gram-negative bacteria.	tetracycline
contig00009	102280	103767	tolC	0/0	100.0	98.2	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan
contig00049	24764	25930	ugd	0/0	100.0	96.0	U00096:2099613-2098446	PmrE is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin	peptide
contig00002	25204	26847	yojI	0/0	100.0	97.4	U00096.3:2308615-2306971	YojI mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. YojI is capable of pumping out microcin molecules. The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI.	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00087	1505	2293	(AGly)aadA5	0/0	100.0	100.0	AF137361:64-852	(AGly)aadA5	NA
contig00107	887	1690	(AGly)strA	0/0	100.0	99.9	AB366441:22458-23261	(AGly)strA	NA
contig00107	51	887	(AGly)strB	0/0	100.0	99.9	FJ474091:264-1100	(AGly)strB	NA
contig00037	13287	14420	(Bla)AmpC2_Ecoli	0/0	100.0	97.8	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00010	51334	52491	(Bla)ampH_Ecoli	0/0	100.0	97.1	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00142	247	1122	(Bla)blaCTX-M-27	0/0	100.0	100.0	AY156923:1-876	(Bla)blaCTX-M-27	NA
contig00071	10414	11274	(Bla)blaTEM-105	0/0	100.0	99.9	AF516720:215-1075	(Bla)blaTEM-105	NA
contig00017	62249	64150	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100.0	98.7	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA
contig00087	2840	3679	(Sul)sul1	0/0	100.0	100.0	AF071413:6700-7539	(Sul)sul1	NA
contig00107	1751	2566	(Sul)sul2	0/0	100.0	100.0	EU360945:1617-2432	(Sul)sul2	NA
contig00121	633	1907	(Tet)tetA	0/0	100.0	100.0	JX424423:94438-95712	(Tet)tetA	NA
contig00121	1	602	(Tet)tetR	1/24	92.5	96.2	HF545434:53576-54226	(Tet)tetR	NA
contig00087	901	1374	(Tmt)dfrA17	0/0	100.0	100.0	AB126604:98-571	(Tmt)dfrA17	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00087	1505	2293	aadA5	0/0	100	100.0	NG_047357.1	ANT(3’’)-Ia family aminoglycoside nucleotidyltransferase AadA5	STREPTOMYCIN
contig00107	887	1714	aph(3’’)-Ib	0/0	100	100.0	NG_056002.2	aminoglycoside O-phosphotransferase APH(3’’)-Ib	STREPTOMYCIN
contig00107	51	887	aph(6)-Id	0/0	100	100.0	NG_047466.1	aminoglycoside O-phosphotransferase APH(6)-Id	STREPTOMYCIN
contig00142	247	1122	blaCTX-M-27	0/0	100	100.0	NG_048976.1	class A extended-spectrum beta-lactamase CTX-M-27	CEPHALOSPORIN
contig00037	13287	14420	blaEC-5	0/0	100	99.5	NG_049085.1	cephalosporin-hydrolyzing class C beta-lactamase EC-5	CEPHALOSPORIN
contig00071	10414	11274	blaTEM-1	0/0	100	100.0	NG_050145.1	class A broad-spectrum beta-lactamase TEM-1	BETA-LACTAM
contig00087	901	1374	dfrA17	0/0	100	99.8	NG_047710.1	trimethoprim-resistant dihydrofolate reductase DfrA17	TRIMETHOPRIM
contig00087	2840	3679	sul1	0/0	100	100.0	NG_048082.1	sulfonamide-resistant dihydropteroate synthase Sul1	SULFONAMIDE
contig00107	1751	2566	sul2	0/0	100	100.0	NG_051852.1	sulfonamide-resistant dihydropteroate synthase Sul2	SULFONAMIDE
contig00121	708	1907	tet(A)	0/0	100	100.0	NG_048154.1	tetracycline efflux MFS transporter Tet(A)	TETRACYCLINE

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00010	140413	141606	ACRA	0/0	100.0	99.1	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00010	137241	140390	ACRB	0/0	100.0	98.8	MEG_401	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRB	NA
contig00006	127119	130232	ACRD	0/0	100.0	98.7	MEG_407	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ACRD	NA
contig00008	149305	150462	ACRE	0/0	100.0	98.8	MEG_408	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRE	NA
contig00008	150474	153578	ACRF	0/0	100.0	96.6	MEG_409	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRF	NA
contig00008	148244	148906	ACRS	0/0	100.0	98.3	MEG_415	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS	NA
contig00010	51334	52491	AMPH	0/0	100.0	97.1	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00087	1505	2293	ANT3-DPRIME	0/0	100.0	100.0	MEG_928	Drugs:Aminoglycosides:Aminoglycoside_O-nucleotidyltransferases:ANT3-DPRIME	NA
contig00107	887	1714	APH3-DPRIME	0/0	100.0	100.0	MEG_1019	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH3-DPRIME	NA
contig00107	51	887	APH6	0/0	100.0	100.0	MEG_1084	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH6	NA
contig00002	189094	190946	ASMA	0/0	100.0	97.6	MEG_1180	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:ASMA	NA
contig00009	129450	130269	BACA	0/0	99.8	98.5	MEG_1189	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00002	166453	167174	BAER	0/0	99.9	97.1	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00002	167171	168574	BAES	0/0	100.0	90.5	MEG_1193	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES	NA
contig00002	50480	51670	BCR	0/0	100.0	96.6	MEG_1210	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR	NA
contig00037	13287	14420	BLAEC	0/0	100.0	99.5	MEG_1275	Drugs:betalactams:Class_C_betalactamases:BLAEC	NA
contig00013	65995	66693	CPXAR	0/0	100.0	98.1	MEG_2118	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00013	66690	68057	CPXAR	0/0	99.6	99.0	MEG_2121	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00007	15089	15721	CRP	0/0	100.0	99.2	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00142	225	1126	CTX	0/0	99.8	99.8	MEG_2401	Drugs:betalactams:Class_A_betalactamases:CTX	NA
contig00087	901	1374	DFRA	0/0	100.0	100.0	MEG_2547	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00005	47612	48784	EMRA	0/0	100.0	98.0	MEG_2722	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA	NA
contig00005	48801	50339	EMRB	0/0	100.0	98.4	MEG_2725	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRB	NA
contig00003	108145	109335	EMRD	0/0	100.0	97.6	MEG_2729	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD	NA
contig00078	5717	6880	EMRK	0/0	100.0	97.4	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig00005	46955	47485	EMRR	0/0	100.0	98.5	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00078	4179	5717	EMRY	0/0	100.0	97.7	MEG_2736	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRY	NA
contig00033	17540	19183	EPTA	0/0	100.0	91.4	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig00058	1556	2284	GADW	0/0	100.0	100.0	MEG_3082	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig00058	363	1187	GADX	0/0	100.0	93.9	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00026	22379	22792	HNS	0/0	100.0	99.3	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00017	3031	3703	KDPE	0/0	99.3	95.5	MEG_3448	Drugs:Aminoglycosides:Aminoglycoside_efflux_pumps:KDPE	NA
contig00001	221588	221977	MARA	0/0	100.0	99.0	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00001	221992	222426	MARR	0/0	100.0	98.2	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00012	29918	31150	MDFA	0/0	100.0	97.9	MEG_3737	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDFA	NA
contig00002	176187	177434	MDTA	0/0	100.0	95.6	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00002	173065	176187	MDTB	0/0	100.0	96.2	MEG_3747	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTB	NA
contig00002	169987	173064	MDTC	0/0	100.0	94.0	MEG_3749	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTC	NA
contig00058	5785	6942	MDTE	0/0	100.0	98.5	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00058	2647	5760	MDTF	0/0	100.0	97.3	MEG_3752	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTF	NA
contig00016	91892	93118	MDTG	0/0	100.0	98.5	MEG_3753	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig00016	82055	83263	MDTH	0/0	100.0	98.3	MEG_3755	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTH	NA
contig00001	190694	191023	MDTI	0/0	100.0	98.8	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00001	190342	190707	MDTJ	0/0	100.0	98.4	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00001	123380	124752	MDTK	0/0	99.9	97.7	MEG_3759	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:MDTK	NA
contig00023	81590	82822	MDTM	0/0	100.0	95.0	MEG_3761	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTM	NA
contig00052	12253	13284	MDTN	0/0	100.0	96.2	MEG_3763	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN	NA
contig00052	10202	12253	MDTO	0/0	100.0	97.1	MEG_3764	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTO	NA
contig00052	8739	10205	MDTP	0/0	100.0	97.6	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig00004	103917	105665	MSBA	0/0	100.0	98.1	MEG_4061	Drugs:Multi-drug_resistance:Multi-drug_ABC_efflux_pumps:MSBA	NA
contig00019	28735	29067	MVRC	0/0	100.0	92.2	MEG_4103	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MVRC	NA
contig00017	62249	64150	PBP2	0/0	100.0	98.7	MEG_5400	Drugs:betalactams:Penicillin_binding_protein:PBP2	NA
contig00027	10123	11091	PMRF	0/0	100.0	97.6	MEG_5801	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF	NA
contig00023	22114	22983	ROBA	0/0	100.0	99.0	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00032	19203	19525	SOXS	0/0	99.7	98.1	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00087	2839	3806	SULI	0/0	100.0	100.0	MEG_6615	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULI	NA
contig00107	1751	2566	SULII	0/0	100.0	100.0	MEG_6617	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULII	NA
contig00071	10396	11641	TEM	0/0	98.3	99.4	MEG_6875	Drugs:betalactams:Class_A_betalactamases:TEM	NA
contig00121	633	1907	TETA	0/0	100.0	100.0	MEG_7024	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETA	NA
contig00049	24764	25930	UGD	0/0	100.0	96.0	MEG_7328	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:UGD	NA
contig00002	25204	26847	YOGI	0/0	100.0	97.4	MEG_7842	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:YOGI	NA

ID011

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00061	1696	2556	aac(3)-IIa_1	0/0	100.0	99.8	X51534	aac(3)-IIa	Gentamicin, Tobramycin
contig00066	1540	2139	aac(6’)-Ib-cr_1	0/0	100.0	100.0	DQ303918	aac(6’)-Ib-cr	Ciprofloxacin
contig00048	1303	2091	aadA5_1	0/0	100.0	100.0	AF137361	aadA5	Streptomycin
contig00058	961	1764	aph(3’’)-Ib_5	0/0	100.0	100.0	AF321551	aph(3’’)-Ib	Streptomycin
contig00058	125	961	aph(6)-Id_1	0/0	100.0	99.9	M28829	aph(6)-Id	Streptomycin
contig00051	2407	3282	blaCTX-M-15_1	0/0	100.0	100.0	AY044436	blaCTX-M-15	Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig00066	579	1409	blaOXA-1_1	0/0	100.0	100.0	HQ170510	blaOXA-1	Amoxicillin, Amoxicillin+Clavulanic_acid, Ampicillin, Ampicillin+Clavulanic_acid, Cefepime, Piperacillin, Piperacillin+Tazobactam
contig00048	699	1172	dfrA17_1	0/0	100.0	100.0	FJ460238	dfrA17	Trimethoprim
contig00014	29919	31151	mdf(A)_1	0/0	100.0	97.8	Y08743	mdf(A)
contig00076	68	905	mph(A)_1	0/0	92.5	100.0	D16251	mph(A)	Erythromycin, Azithromycin, Spiramycin, Telithromycin
contig00048	2611	3477	sul1_5	0/0	100.0	99.9	EU780013	sul1	Sulfamethoxazole
contig00058	1825	2640	sul2_2	0/0	100.0	100.0	AY034138	sul2	Sulfamethoxazole
contig00049	5808	7054	tet(A)_6	0/0	97.8	100.0	AF534183	tet(A)	Doxycycline, Tetracycline

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00061	1696	2556	AAC(3)-IIe	0/0	100.0	99.5	EU022315.1:0-861	AAC(3)-IIe is a plasmid-encoded aminoglycoside acetyltransferase in E. coli	aminoglycoside
contig00066	1540	2139	AAC(6’)-Ib-cr	0/0	100.0	100.0	DQ303918:0-600	AAC(6’)-Ib-cr is an aminoglycoside acetyltransferase encoded by plasmids transposons integrons in Enterobacteriaceae. The aac(6’)-Ib-cr variant gene can induce resistance against aminoglycoside and fluoroquinolone simultaneously	aminoglycoside, fluoroquinolone
contig00048	1303	2091	aadA5	0/0	100.0	100.0	AF137361:63-852	aadA5 is an aminoglycoside nucleotidyltransferase gene encoded by plasmids transposons and integrons in E. coli K. pneumoniae Kluyvera georgiana P. aeruginosa and E. cloacae	aminoglycoside
contig00002	279235	282384	acrB	0/0	100.0	98.8	U00096.3:484403-481253	Protein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug/proton antiporter.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00001	127109	130222	acrD	0/0	100.0	98.7	AP009048.1:2586250-2589364	AcrD is an aminoglycoside efflux pump expressed in E. coli. Its expression can be induced by indole and is regulated by baeRS and cpxAR.	aminoglycoside
contig00012	150532	151689	acrE	0/0	100.0	98.7	U00096:3413863-3415021	AcrE is a membrane fusion protein similar to AcrA.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00012	151701	154805	acrF	0/0	100.0	96.6	U00096:3415032-3418137	AcrF is a inner membrane transporter similar to AcrB.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00012	149471	150133	acrS	0/0	100.0	98.3	U00096:3413465-3412802	AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.	cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00058	961	1764	APH(3’’)-Ib	0/0	100.0	99.8	AF313472:15593-16397	APH(3’’)-Ib is an aminoglycoside phosphotransferase encoded by plasmids transposons integrative conjugative elements and chromosomes in Enterobacteriaceae and Pseudomonas spp.	aminoglycoside
contig00058	125	961	APH(6)-Id	0/0	100.0	99.8	AF024602:3155-3992	APH(6)-Id is an aminoglycoside phosphotransferase encoded by plasmids integrative conjugative elements and chromosomal genomic islands in K. pneumoniae Salmonella spp. E. coli Shigella flexneri Providencia alcalifaciens Pseudomonas spp. V. cholerae Edwardsiella tarda Pasteurella multocida and Aeromonas bestiarum	aminoglycoside
contig00007	52237	53056	bacA	0/0	99.8	98.3	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00001	566555	567276	baeR	0/0	99.9	97.1	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00001	567273	568676	baeS	0/0	100.0	90.5	AP009048:2165012-2166416	BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.	aminocoumarin, aminoglycoside
contig00016	66690	68057	cpxA	0/0	99.6	98.5	BA000007.3:4905062-4903688	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	aminocoumarin, aminoglycoside
contig00008	15089	15721	CRP	0/0	100.0	99.2	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00051	2407	3282	CTX-M-15	0/0	100.0	100.0	AY044436:1435-2311	CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family	cephalosporin
contig00048	699	1172	dfrA17	0/0	100.0	100.0	DQ838665:0-474	dfrA17 is an integron-encoded dihydrofolate reductase found in Escherichia coli	diaminopyrimidine
contig00006	60267	61439	emrA	0/0	100.0	98.0	AP009048:2810082-2811255	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	fluoroquinolone
contig00006	61456	62994	emrB	0/0	100.0	98.4	U00096:2812615-2814154	emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin.	fluoroquinolone
contig00001	222937	223992	emrK	0/0	100.0	97.7	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00006	59610	60140	emrR	0/0	100.0	98.5	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00001	223992	225530	emrY	0/0	100.0	97.7	D78168:1591-3130	emrY is a multidrug transport that moves substrates across the inner membrane of the Gram-negative E. coli. It is a homolog of emrB.	tetracycline
contig00009	146391	148034	eptA	0/0	100.0	91.4	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00002	278019	279212	Escherichia_coli_acrA	0/0	100.0	99.1	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00022	48091	49224	Escherichia_coli_ampC	0/0	100.0	97.8	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00002	367134	368291	Escherichia_coli_ampH	0/0	100.0	97.1	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig00013	28735	29067	Escherichia_coli_emrE	0/0	100.0	92.2	Z11877.1:485-818	Member of the small MDR (multidrug resistance) family of transporters, in Escherichia coli this protein provides resistance against a number of positively charged compounds including ethidium bromide and erythromycin, proton-dependent secondary transporter which exchanges protons for compound translocation	macrolide
contig00014	29919	31151	Escherichia_coli_mdfA	0/0	100.0	96.3	JQ394987:0-1233	Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter.	benzalkonium_chloride, rhodamine, tetracycline
contig00001	221799	222413	evgA	0/0	100.0	99.0	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00001	218201	221794	evgS	0/0	100.0	96.3	U00096:2484373-2487967	EvgS is a sensor protein that phosphorylates the regulatory protein EvgA. evgS corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	fluoroquinolone, macrolide, penam, tetracycline
contig00008	188688	189416	gadW	0/0	100.0	100.0	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig00008	189785	190609	gadX	0/0	100.0	93.9	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00020	39527	39940	H-NS	0/0	100.0	99.3	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00002	53943	54615	kdpE	0/0	99.3	95.5	U00096.3:721733-721055	kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding.	aminoglycoside
contig00019	29733	30116	marA	0/0	100.0	99.0	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00001	576289	577536	mdtA	0/0	100.0	95.6	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00001	573167	576289	mdtB	0/0	100.0	96.2	U00096:2155262-2158385	MdtB is a transporter that forms a heteromultimer complex with MdtC to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex.	aminocoumarin
contig00001	570089	573166	mdtC	0/0	100.0	94.0	U00096:2158385-2161463	MdtC is a transporter that forms a heteromultimer complex with MdtB to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex. In the absence of MdtB MdtC can form a homomultimer complex that results in a functioning efflux complex with a narrower drug specificity. mdtC corresponds to 3 loci in Pseudomonas aeruginosa PAO1 (gene name: muxC/muxB) and 3 loci in Pseudomonas aeruginosa LESB58.	aminocoumarin
contig00008	184030	185187	mdtE	0/0	100.0	98.5	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00008	185212	188325	mdtF	0/0	100.0	97.3	U00096:3660413-3663527	MdtF is the multidrug inner membrane transporter for the MdtEF-TolC efflux complex.	fluoroquinolone, macrolide, penam
contig00011	91787	93013	mdtG	0/0	100.0	98.4	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00011	81950	83158	mdtH	0/0	100.0	98.3	U00096:1125326-1124117	Multidrug resistance protein MdtH	fluoroquinolone
contig00003	306709	307941	mdtM	0/0	100.0	95.0	U00096.3:4568519-4567286	Multidrug resistance protein MdtM	acridine_dye, fluoroquinolone, lincosamide, nucleoside, phenicol
contig00009	116127	117158	mdtN	0/0	100.0	96.2	AP009048.1:4307588-4306556	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	acridine_dye, nucleoside
contig00009	114076	116127	mdtO	0/0	100.0	97.0	AP009048.1:4306557-4304505	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00009	112613	114079	mdtP	0/0	100.0	97.6	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00076	68	905	mphA	0/0	92.5	100.0	D16251.1:2531-1625	The mphA gene encodes for resistance enzyme MPH(2’)-I which preferentially inactivate 14-membered macrolides (e.g.erythromycin telithromycin roxithromycin) over 16-membered macrolides (e.g.tylosin spiramycin). It phosphorylates macrolides at 2’-OH hydroxyl of desosamine sugar of macrolides in a GTP-dependent manner.	macrolide
contig00015	45415	47163	msbA	0/0	100.0	98.1	U00096.3:966620-968369	MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability.	nitroimidazole
contig00066	579	1409	OXA-1	0/0	100.0	100.0	JN420336.1:2230-1399	OXA-1 is a beta-lactamase found in E. coli	cephalosporin, penam
contig00001	332550	333518	pmrF	0/0	100.0	97.6	U00096:2367070-2368039	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide
contig00048	2638	3477	sul1	0/0	100.0	100.0	JF969163:1053-1893	Sul1 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria. It is linked to other resistance genes of class 1 integrons.	sulfonamide
contig00058	1825	2640	sul2	0/0	100.0	100.0	AY055428.1:21084-20268	Sul2 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria usually found on small plasmids.	sulfonamide
contig00049	5808	7054	tet(A)	0/0	97.8	100.0	AF534183.1:2970-4245	TetA is a tetracycline efflux pump found in many species of Gram-negative bacteria.	tetracycline
contig00007	78739	80226	tolC	0/0	100.0	98.2	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan
contig00001	630632	631798	ugd	0/0	100.0	96.0	U00096:2099613-2098446	PmrE is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin	peptide
contig00001	391723	393366	yojI	0/0	100.0	97.4	U00096.3:2308615-2306971	YojI mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. YojI is capable of pumping out microcin molecules. The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI.	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00061	1696	2556	(AGly)aac3-IIa	0/0	100.0	99.8	X51534:91-951	(AGly)aac3-IIa	NA
contig00048	1303	2091	(AGly)aadA5	0/0	100.0	100.0	AF137361:64-852	(AGly)aadA5	NA
contig00058	961	1764	(AGly)strA	0/0	100.0	99.9	AB366441:22458-23261	(AGly)strA	NA
contig00058	125	961	(AGly)strB	0/0	100.0	99.9	FJ474091:264-1100	(AGly)strB	NA
contig00022	48091	49224	(Bla)AmpC2_Ecoli	0/0	100.0	97.8	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00002	367134	368291	(Bla)ampH_Ecoli	0/0	100.0	97.1	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00051	2407	3282	(Bla)blaCTX-M-15	0/0	100.0	100.0	JQ686199:261-1136	(Bla)blaCTX-M-15	NA
contig00066	579	1409	(Bla)blaOXA-1	0/0	100.0	100.0	JQ682867:1-831	(Bla)blaOXA-1	NA
contig00002	113161	115062	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100.0	98.7	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA
contig00076	68	905	(MLS)mph(A)	0/0	92.5	100.0	DQ445270:1626-2531	(MLS)mph(A)	NA
contig00048	2638	3477	(Sul)sul1	0/0	100.0	100.0	AF071413:6700-7539	(Sul)sul1	NA
contig00058	1825	2640	(Sul)sul2	0/0	100.0	100.0	EU360945:1617-2432	(Sul)sul2	NA
contig00049	5780	7054	(Tet)tetA	0/0	100.0	100.0	JX424423:94438-95712	(Tet)tetA	NA
contig00048	699	1172	(Tmt)dfrA17	0/0	100.0	100.0	AB126604:98-571	(Tmt)dfrA17	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00061	1696	2556	aac(3)-IIe	0/0	100.0	99.8	NG_047244.1	aminoglycoside N-acetyltransferase AAC(3)-IIe	GENTAMICIN
contig00066	1540	2094	aac(6’)-Ib-D181Y	0/0	100.0	99.8	NG_067946.1	AAC(6’)-Ib family aminoglycoside 6’-N-acetyltransferase	AMIKACIN, KANAMYCIN, TOBRAMYCIN
contig00048	1303	2091	aadA5	0/0	100.0	100.0	NG_047357.1	ANT(3’’)-Ia family aminoglycoside nucleotidyltransferase AadA5	STREPTOMYCIN
contig00058	961	1788	aph(3’’)-Ib	0/0	100.0	100.0	NG_056002.2	aminoglycoside O-phosphotransferase APH(3’’)-Ib	STREPTOMYCIN
contig00058	125	961	aph(6)-Id	0/0	100.0	100.0	NG_047466.1	aminoglycoside O-phosphotransferase APH(6)-Id	STREPTOMYCIN
contig00051	2407	3282	blaCTX-M-15	0/0	100.0	100.0	NG_048935.1	class A extended-spectrum beta-lactamase CTX-M-15	CEPHALOSPORIN
contig00022	48091	49224	blaEC-5	0/0	100.0	99.5	NG_049085.1	cephalosporin-hydrolyzing class C beta-lactamase EC-5	CEPHALOSPORIN
contig00066	579	1409	blaOXA-1	0/0	100.0	100.0	NG_049392.1	oxacillin-hydrolyzing class D beta-lactamase OXA-1	CEPHALOSPORIN
contig00048	699	1172	dfrA17	0/0	100.0	99.8	NG_047710.1	trimethoprim-resistant dihydrofolate reductase DfrA17	TRIMETHOPRIM
contig00076	68	905	mph(A)	0/0	92.5	100.0	NG_047985.1	Mph(A) family macrolide 2’-phosphotransferase	MACROLIDE
contig00048	2638	3477	sul1	0/0	100.0	100.0	NG_048082.1	sulfonamide-resistant dihydropteroate synthase Sul1	SULFONAMIDE
contig00058	1825	2640	sul2	0/0	100.0	100.0	NG_051852.1	sulfonamide-resistant dihydropteroate synthase Sul2	SULFONAMIDE
contig00049	5780	6979	tet(A)	0/0	100.0	100.0	NG_048154.1	tetracycline efflux MFS transporter Tet(A)	TETRACYCLINE

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00061	1696	2556	AAC3	0/0	100.0	99.8	MEG_44	Drugs:Aminoglycosides:Aminoglycoside_N-acetyltransferases:AAC3	NA
contig00002	278019	279212	ACRA	0/0	100.0	99.1	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00002	279235	282384	ACRB	0/0	100.0	98.8	MEG_401	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRB	NA
contig00001	127109	130222	ACRD	0/0	100.0	98.7	MEG_407	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ACRD	NA
contig00012	150532	151689	ACRE	0/0	100.0	98.7	MEG_408	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRE	NA
contig00012	151701	154805	ACRF	0/0	100.0	96.6	MEG_409	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRF	NA
contig00012	149471	150133	ACRS	0/0	100.0	98.3	MEG_415	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS	NA
contig00002	367134	368291	AMPH	0/0	100.0	97.1	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00048	1303	2091	ANT3-DPRIME	0/0	100.0	100.0	MEG_928	Drugs:Aminoglycosides:Aminoglycoside_O-nucleotidyltransferases:ANT3-DPRIME	NA
contig00058	961	1788	APH3-DPRIME	0/0	100.0	100.0	MEG_1019	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH3-DPRIME	NA
contig00058	125	961	APH6	0/0	100.0	100.0	MEG_1084	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH6	NA
contig00001	589196	591048	ASMA	0/0	100.0	97.6	MEG_1180	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:ASMA	NA
contig00007	52237	53056	BACA	0/0	99.8	98.5	MEG_1189	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00001	566555	567276	BAER	0/0	99.9	97.1	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00001	567273	568676	BAES	0/0	100.0	90.5	MEG_1193	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES	NA
contig00001	416999	418189	BCR	0/0	100.0	96.6	MEG_1210	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR	NA
contig00022	48091	49224	BLAEC	0/0	100.0	99.5	MEG_1275	Drugs:betalactams:Class_C_betalactamases:BLAEC	NA
contig00016	65995	66693	CPXAR	0/0	100.0	98.1	MEG_2118	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00016	66690	68057	CPXAR	0/0	99.6	99.0	MEG_2121	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00008	15089	15721	CRP	0/0	100.0	99.2	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00048	699	1172	DFRA	0/0	100.0	100.0	MEG_2547	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00006	60267	61439	EMRA	0/0	100.0	98.0	MEG_2722	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA	NA
contig00006	61456	62994	EMRB	0/0	100.0	98.4	MEG_2725	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRB	NA
contig00004	194231	195421	EMRD	0/0	100.0	97.5	MEG_2729	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD	NA
contig00001	222829	223992	EMRK	0/0	100.0	97.4	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig00006	59610	60140	EMRR	0/0	100.0	98.5	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00001	223992	225530	EMRY	0/0	100.0	97.7	MEG_2736	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRY	NA
contig00009	146391	148034	EPTA	0/0	100.0	91.4	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig00001	218201	221794	EVGS	0/0	100.0	97.4	MEG_2869	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EVGS	NA
contig00008	188688	189416	GADW	0/0	100.0	100.0	MEG_3082	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig00008	189785	190609	GADX	0/0	100.0	93.9	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00020	39527	39940	HNS	0/0	100.0	99.3	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00002	53943	54615	KDPE	0/0	99.3	95.5	MEG_3448	Drugs:Aminoglycosides:Aminoglycoside_efflux_pumps:KDPE	NA
contig00019	29727	30116	MARA	0/0	100.0	99.0	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00019	29278	29712	MARR	0/0	100.0	98.2	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00014	29919	31151	MDFA	0/0	100.0	97.9	MEG_3737	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDFA	NA
contig00001	576289	577536	MDTA	0/0	100.0	95.6	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00001	573167	576289	MDTB	0/0	100.0	96.2	MEG_3747	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTB	NA
contig00001	570089	573166	MDTC	0/0	100.0	94.0	MEG_3749	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTC	NA
contig00008	184030	185187	MDTE	0/0	100.0	98.5	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00008	185212	188325	MDTF	0/0	100.0	97.3	MEG_3752	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTF	NA
contig00011	91787	93013	MDTG	0/0	100.0	98.5	MEG_3753	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig00011	81950	83158	MDTH	0/0	100.0	98.3	MEG_3755	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTH	NA
contig00019	60681	61010	MDTI	0/0	100.0	98.8	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00019	60997	61362	MDTJ	0/0	100.0	98.4	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00005	191249	192621	MDTK	0/0	99.9	97.7	MEG_3759	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:MDTK	NA
contig00003	306709	307941	MDTM	0/0	100.0	95.0	MEG_3761	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTM	NA
contig00009	116127	117158	MDTN	0/0	100.0	96.2	MEG_3763	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN	NA
contig00009	114076	116127	MDTO	0/0	100.0	97.0	MEG_3764	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTO	NA
contig00009	112613	114079	MDTP	0/0	100.0	97.6	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig00076	68	905	MPHA	0/0	92.5	100.0	MEG_4029	Drugs:MLS:Macrolide_phosphotransferases:MPHA	NA
contig00015	45415	47163	MSBA	0/0	100.0	98.1	MEG_4061	Drugs:Multi-drug_resistance:Multi-drug_ABC_efflux_pumps:MSBA	NA
contig00013	28735	29067	MVRC	0/0	100.0	92.2	MEG_4103	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MVRC	NA
contig00066	579	1409	OXA	0/0	100.0	100.0	MEG_4980	Drugs:betalactams:Class_D_betalactamases:OXA	NA
contig00002	113161	115062	PBP2	0/0	100.0	98.7	MEG_5400	Drugs:betalactams:Penicillin_binding_protein:PBP2	NA
contig00001	332550	333518	PMRF	0/0	100.0	97.6	MEG_5801	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF	NA
contig00003	247233	248102	ROBA	0/0	100.0	99.0	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00009	84260	84582	SOXS	0/0	99.7	98.1	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00048	2637	3604	SULI	0/0	100.0	100.0	MEG_6615	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULI	NA
contig00058	1825	2640	SULII	0/0	100.0	100.0	MEG_6617	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULII	NA
contig00049	5780	7054	TETA	0/0	100.0	100.0	MEG_7024	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETA	NA
contig00001	630632	631798	UGD	0/0	100.0	96.0	MEG_7328	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:UGD	NA
contig00001	391723	393366	YOGI	0/0	100.0	97.4	MEG_7842	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:YOGI	NA

ID013I

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00084	1696	2556	aac(3)-IIa_1	0/0	100.0	99.8	X51534	aac(3)-IIa	Gentamicin, Tobramycin
contig00091	1540	2139	aac(6’)-Ib-cr_1	0/0	100.0	100.0	DQ303918	aac(6’)-Ib-cr	Ciprofloxacin
contig00062	1638	2426	aadA5_1	0/0	100.0	100.0	AF137361	aadA5	Streptomycin
contig00080	859	1662	aph(3’’)-Ib_5	0/0	100.0	100.0	AF321551	aph(3’’)-Ib	Streptomycin
contig00080	23	859	aph(6)-Id_1	0/0	100.0	99.9	M28829	aph(6)-Id	Streptomycin
contig00100	48	923	blaCTX-M-15_1	0/0	100.0	100.0	AY044436	blaCTX-M-15	Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig00091	579	1409	blaOXA-1_1	0/0	100.0	100.0	HQ170510	blaOXA-1	Amoxicillin, Amoxicillin+Clavulanic_acid, Ampicillin, Ampicillin+Clavulanic_acid, Cefepime, Piperacillin, Piperacillin+Tazobactam
contig00050	15590	16450	blaTEM-1B_1	0/0	100.0	100.0	AY458016	blaTEM-1B	Amoxicillin, Ampicillin, Cephalothin, Piperacillin, Ticarcillin
contig00062	1034	1507	dfrA17_1	0/0	100.0	100.0	FJ460238	dfrA17	Trimethoprim
contig00011	29926	31158	mdf(A)_1	0/0	100.0	97.8	Y08743	mdf(A)
contig00101	69	990	mph(A)_2	1/1	100.0	99.7	U36578	mph(A)	Erythromycin, Azithromycin, Spiramycin, Telithromycin
contig00062	2946	3812	sul1_5	0/0	100.0	99.9	EU780013	sul1	Sulfamethoxazole
contig00080	1723	2538	sul2_2	0/0	100.0	100.0	AY034138	sul2	Sulfamethoxazole
contig00078	914	2160	tet(A)_6	0/0	97.8	100.0	AF534183	tet(A)	Doxycycline, Tetracycline

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00084	1696	2556	AAC(3)-IIe	0/0	100.0	99.5	EU022315.1:0-861	AAC(3)-IIe is a plasmid-encoded aminoglycoside acetyltransferase in E. coli	aminoglycoside
contig00091	1540	2139	AAC(6’)-Ib-cr	0/0	100.0	100.0	DQ303918:0-600	AAC(6’)-Ib-cr is an aminoglycoside acetyltransferase encoded by plasmids transposons integrons in Enterobacteriaceae. The aac(6’)-Ib-cr variant gene can induce resistance against aminoglycoside and fluoroquinolone simultaneously	aminoglycoside, fluoroquinolone
contig00062	1638	2426	aadA5	0/0	100.0	100.0	AF137361:63-852	aadA5 is an aminoglycoside nucleotidyltransferase gene encoded by plasmids transposons and integrons in E. coli K. pneumoniae Kluyvera georgiana P. aeruginosa and E. cloacae	aminoglycoside
contig00001	268024	271173	acrB	0/0	100.0	98.8	U00096.3:484403-481253	Protein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug/proton antiporter.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00004	99467	102580	acrD	0/0	100.0	98.7	AP009048.1:2586250-2589364	AcrD is an aminoglycoside efflux pump expressed in E. coli. Its expression can be induced by indole and is regulated by baeRS and cpxAR.	aminoglycoside
contig00009	149304	150461	acrE	0/0	100.0	98.8	U00096:3413863-3415021	AcrE is a membrane fusion protein similar to AcrA.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00009	150473	153577	acrF	0/0	100.0	96.6	U00096:3415032-3418137	AcrF is a inner membrane transporter similar to AcrB.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00009	148243	148905	acrS	0/0	100.0	98.3	U00096:3413465-3412802	AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.	cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00080	859	1662	APH(3’’)-Ib	0/0	100.0	99.8	AF313472:15593-16397	APH(3’’)-Ib is an aminoglycoside phosphotransferase encoded by plasmids transposons integrative conjugative elements and chromosomes in Enterobacteriaceae and Pseudomonas spp.	aminoglycoside
contig00080	23	859	APH(6)-Id	0/0	100.0	99.8	AF024602:3155-3992	APH(6)-Id is an aminoglycoside phosphotransferase encoded by plasmids integrative conjugative elements and chromosomal genomic islands in K. pneumoniae Salmonella spp. E. coli Shigella flexneri Providencia alcalifaciens Pseudomonas spp. V. cholerae Edwardsiella tarda Pasteurella multocida and Aeromonas bestiarum	aminoglycoside
contig00006	52237	53056	bacA	0/0	99.8	98.3	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00027	23560	24281	baeR	0/0	99.9	97.1	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00027	22160	23563	baeS	0/0	100.0	90.5	AP009048:2165012-2166416	BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.	aminocoumarin, aminoglycoside
contig00014	66690	68057	cpxA	0/0	99.6	98.5	BA000007.3:4905062-4903688	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	aminocoumarin, aminoglycoside
contig00008	15089	15721	CRP	0/0	100.0	99.2	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00100	48	923	CTX-M-15	0/0	100.0	100.0	AY044436:1435-2311	CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family	cephalosporin
contig00062	1034	1507	dfrA17	0/0	100.0	100.0	DQ838665:0-474	dfrA17 is an integron-encoded dihydrofolate reductase found in Escherichia coli	diaminopyrimidine
contig00035	48077	49249	emrA	0/0	100.0	98.0	AP009048:2810082-2811255	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	fluoroquinolone
contig00035	49266	50804	emrB	0/0	100.0	98.4	U00096:2812615-2814154	emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin.	fluoroquinolone
contig00004	5697	6752	emrK	0/0	100.0	97.7	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00035	47420	47950	emrR	0/0	100.0	98.5	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00004	4159	5697	emrY	0/0	100.0	97.7	D78168:1591-3130	emrY is a multidrug transport that moves substrates across the inner membrane of the Gram-negative E. coli. It is a homolog of emrB.	tetracycline
contig00020	72758	74401	eptA	0/0	100.0	91.4	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00001	266808	268001	Escherichia_coli_acrA	0/0	100.0	99.1	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00028	48092	49225	Escherichia_coli_ampC	0/0	100.0	97.8	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00001	355923	357080	Escherichia_coli_ampH	0/0	100.0	97.1	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig00012	28735	29067	Escherichia_coli_emrE	0/0	100.0	92.2	Z11877.1:485-818	Member of the small MDR (multidrug resistance) family of transporters, in Escherichia coli this protein provides resistance against a number of positively charged compounds including ethidium bromide and erythromycin, proton-dependent secondary transporter which exchanges protons for compound translocation	macrolide
contig00011	29926	31158	Escherichia_coli_mdfA	0/0	100.0	96.3	JQ394987:0-1233	Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter.	benzalkonium_chloride, rhodamine, tetracycline
contig00004	7276	7890	evgA	0/0	100.0	99.0	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00004	7895	11488	evgS	0/0	100.0	96.3	U00096:2484373-2487967	EvgS is a sensor protein that phosphorylates the regulatory protein EvgA. evgS corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	fluoroquinolone, macrolide, penam, tetracycline
contig00008	188688	189416	gadW	0/0	100.0	100.0	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig00008	189785	190609	gadX	0/0	100.0	93.9	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00025	39527	39940	H-NS	0/0	100.0	99.3	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00001	42732	43404	kdpE	0/0	99.3	95.5	U00096.3:721733-721055	kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding.	aminoglycoside
contig00002	289457	289840	marA	0/0	100.0	99.0	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00027	13300	14547	mdtA	0/0	100.0	95.6	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00027	14547	17669	mdtB	0/0	100.0	96.2	U00096:2155262-2158385	MdtB is a transporter that forms a heteromultimer complex with MdtC to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex.	aminocoumarin
contig00027	17670	20747	mdtC	0/0	100.0	94.0	U00096:2158385-2161463	MdtC is a transporter that forms a heteromultimer complex with MdtB to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex. In the absence of MdtB MdtC can form a homomultimer complex that results in a functioning efflux complex with a narrower drug specificity. mdtC corresponds to 3 loci in Pseudomonas aeruginosa PAO1 (gene name: muxC/muxB) and 3 loci in Pseudomonas aeruginosa LESB58.	aminocoumarin
contig00008	184030	185187	mdtE	0/0	100.0	98.5	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00008	185212	188325	mdtF	0/0	100.0	97.3	U00096:3660413-3663527	MdtF is the multidrug inner membrane transporter for the MdtEF-TolC efflux complex.	fluoroquinolone, macrolide, penam
contig00003	122019	123245	mdtG	0/0	100.0	98.4	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00003	112182	113390	mdtH	0/0	100.0	98.3	U00096:1125326-1124117	Multidrug resistance protein MdtH	fluoroquinolone
contig00030	38717	39949	mdtM	0/0	100.0	95.0	U00096.3:4568519-4567286	Multidrug resistance protein MdtM	acridine_dye, fluoroquinolone, lincosamide, nucleoside, phenicol
contig00020	42485	43516	mdtN	0/0	100.0	96.2	AP009048.1:4307588-4306556	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	acridine_dye, nucleoside
contig00020	40434	42485	mdtO	0/0	100.0	97.0	AP009048.1:4306557-4304505	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00020	38971	40437	mdtP	0/0	100.0	97.6	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00101	69	974	mphA	0/0	100.0	100.0	D16251.1:2531-1625	The mphA gene encodes for resistance enzyme MPH(2’)-I which preferentially inactivate 14-membered macrolides (e.g.erythromycin telithromycin roxithromycin) over 16-membered macrolides (e.g.tylosin spiramycin). It phosphorylates macrolides at 2’-OH hydroxyl of desosamine sugar of macrolides in a GTP-dependent manner.	macrolide
contig00003	247892	249640	msbA	0/0	100.0	98.1	U00096.3:966620-968369	MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability.	nitroimidazole
contig00091	579	1409	OXA-1	0/0	100.0	100.0	JN420336.1:2230-1399	OXA-1 is a beta-lactamase found in E. coli	cephalosporin, penam
contig00007	90060	91028	pmrF	0/0	100.0	97.6	U00096:2367070-2368039	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide
contig00062	2973	3812	sul1	0/0	100.0	100.0	JF969163:1053-1893	Sul1 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria. It is linked to other resistance genes of class 1 integrons.	sulfonamide
contig00080	1723	2538	sul2	0/0	100.0	100.0	AY055428.1:21084-20268	Sul2 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria usually found on small plasmids.	sulfonamide
contig00050	15590	16450	TEM-1	0/0	100.0	99.9	AL513383:161910-162771	TEM-1 is a broad-spectrum beta-lactamase found in many Gram-negative bacteria. Confers resistance to penicillins and first generation cephalosphorins.	cephalosporin, monobactam, penam, penem
contig00078	914	2160	tet(A)	0/0	97.8	100.0	AF534183.1:2970-4245	TetA is a tetracycline efflux pump found in many species of Gram-negative bacteria.	tetracycline
contig00006	78739	80226	tolC	0/0	100.0	98.2	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan
contig00034	39758	40924	ugd	0/0	100.0	96.0	U00096:2099613-2098446	PmrE is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin	peptide
contig00007	30212	31855	yojI	0/0	100.0	97.4	U00096.3:2308615-2306971	YojI mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. YojI is capable of pumping out microcin molecules. The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI.	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00084	1696	2556	(AGly)aac3-IIa	0/0	100.0	99.8	X51534:91-951	(AGly)aac3-IIa	NA
contig00062	1638	2426	(AGly)aadA5	0/0	100.0	100.0	AF137361:64-852	(AGly)aadA5	NA
contig00080	859	1662	(AGly)strA	0/0	100.0	99.9	AB366441:22458-23261	(AGly)strA	NA
contig00080	23	859	(AGly)strB	0/0	100.0	99.9	FJ474091:264-1100	(AGly)strB	NA
contig00028	48092	49225	(Bla)AmpC2_Ecoli	0/0	100.0	97.8	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00001	355923	357080	(Bla)ampH_Ecoli	0/0	100.0	97.1	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00100	48	923	(Bla)blaCTX-M-15	0/0	100.0	100.0	JQ686199:261-1136	(Bla)blaCTX-M-15	NA
contig00091	579	1409	(Bla)blaOXA-1	0/0	100.0	100.0	JQ682867:1-831	(Bla)blaOXA-1	NA
contig00050	15590	16450	(Bla)blaTEM-105	0/0	100.0	99.9	AF516720:215-1075	(Bla)blaTEM-105	NA
contig00001	101950	103851	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100.0	98.7	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA
contig00101	69	974	(MLS)mph(A)	0/0	100.0	100.0	DQ445270:1626-2531	(MLS)mph(A)	NA
contig00062	2973	3812	(Sul)sul1	0/0	100.0	100.0	AF071413:6700-7539	(Sul)sul1	NA
contig00080	1723	2538	(Sul)sul2	0/0	100.0	100.0	EU360945:1617-2432	(Sul)sul2	NA
contig00078	914	2188	(Tet)tetA	0/0	100.0	100.0	JX424423:94438-95712	(Tet)tetA	NA
contig00078	257	883	(Tet)tetR	1/24	96.3	96.3	HF545434:53576-54226	(Tet)tetR	NA
contig00062	1034	1507	(Tmt)dfrA17	0/0	100.0	100.0	AB126604:98-571	(Tmt)dfrA17	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00084	1696	2556	aac(3)-IIe	0/0	100	99.8	NG_047244.1	aminoglycoside N-acetyltransferase AAC(3)-IIe	GENTAMICIN
contig00091	1540	2094	aac(6’)-Ib-D181Y	0/0	100	99.8	NG_067946.1	AAC(6’)-Ib family aminoglycoside 6’-N-acetyltransferase	AMIKACIN, KANAMYCIN, TOBRAMYCIN
contig00062	1638	2426	aadA5	0/0	100	100.0	NG_047357.1	ANT(3’’)-Ia family aminoglycoside nucleotidyltransferase AadA5	STREPTOMYCIN
contig00080	859	1686	aph(3’’)-Ib	0/0	100	100.0	NG_056002.2	aminoglycoside O-phosphotransferase APH(3’’)-Ib	STREPTOMYCIN
contig00080	23	859	aph(6)-Id	0/0	100	100.0	NG_047466.1	aminoglycoside O-phosphotransferase APH(6)-Id	STREPTOMYCIN
contig00100	48	923	blaCTX-M-15	0/0	100	100.0	NG_048935.1	class A extended-spectrum beta-lactamase CTX-M-15	CEPHALOSPORIN
contig00028	48092	49225	blaEC-5	0/0	100	99.5	NG_049085.1	cephalosporin-hydrolyzing class C beta-lactamase EC-5	CEPHALOSPORIN
contig00091	579	1409	blaOXA-1	0/0	100	100.0	NG_049392.1	oxacillin-hydrolyzing class D beta-lactamase OXA-1	CEPHALOSPORIN
contig00050	15590	16450	blaTEM-1	0/0	100	100.0	NG_050145.1	class A broad-spectrum beta-lactamase TEM-1	BETA-LACTAM
contig00062	1034	1507	dfrA17	0/0	100	99.8	NG_047710.1	trimethoprim-resistant dihydrofolate reductase DfrA17	TRIMETHOPRIM
contig00101	69	990	mph(A)	1/1	100	99.7	NG_047986.1	Mph(A) family macrolide 2’-phosphotransferase	MACROLIDE
contig00062	2973	3812	sul1	0/0	100	100.0	NG_048082.1	sulfonamide-resistant dihydropteroate synthase Sul1	SULFONAMIDE
contig00080	1723	2538	sul2	0/0	100	100.0	NG_051852.1	sulfonamide-resistant dihydropteroate synthase Sul2	SULFONAMIDE
contig00078	989	2188	tet(A)	0/0	100	100.0	NG_048154.1	tetracycline efflux MFS transporter Tet(A)	TETRACYCLINE

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00084	1696	2556	AAC3	0/0	100.0	99.8	MEG_44	Drugs:Aminoglycosides:Aminoglycoside_N-acetyltransferases:AAC3	NA
contig00001	266808	268001	ACRA	0/0	100.0	99.1	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00001	268024	271173	ACRB	0/0	100.0	98.8	MEG_401	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRB	NA
contig00004	99467	102580	ACRD	0/0	100.0	98.7	MEG_407	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ACRD	NA
contig00009	149304	150461	ACRE	0/0	100.0	98.8	MEG_408	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRE	NA
contig00009	150473	153577	ACRF	0/0	100.0	96.6	MEG_409	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRF	NA
contig00009	148243	148905	ACRS	0/0	100.0	98.3	MEG_415	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS	NA
contig00001	355923	357080	AMPH	0/0	100.0	97.1	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00062	1638	2426	ANT3-DPRIME	0/0	100.0	100.0	MEG_928	Drugs:Aminoglycosides:Aminoglycoside_O-nucleotidyltransferases:ANT3-DPRIME	NA
contig00080	859	1686	APH3-DPRIME	0/0	100.0	100.0	MEG_1019	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH3-DPRIME	NA
contig00080	23	859	APH6	0/0	100.0	100.0	MEG_1084	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH6	NA
contig00006	52237	53056	BACA	0/0	99.8	98.5	MEG_1189	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00027	23560	24281	BAER	0/0	99.9	97.1	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00027	22160	23563	BAES	0/0	100.0	90.5	MEG_1193	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES	NA
contig00007	5389	6579	BCR	0/0	100.0	96.6	MEG_1210	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR	NA
contig00028	48092	49225	BLAEC	0/0	100.0	99.5	MEG_1275	Drugs:betalactams:Class_C_betalactamases:BLAEC	NA
contig00014	65995	66693	CPXAR	0/0	100.0	98.1	MEG_2118	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00014	66690	68057	CPXAR	0/0	99.6	99.0	MEG_2121	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00008	15089	15721	CRP	0/0	100.0	99.2	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00062	1034	1507	DFRA	0/0	100.0	100.0	MEG_2547	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00035	48077	49249	EMRA	0/0	100.0	98.0	MEG_2722	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA	NA
contig00035	49266	50804	EMRB	0/0	100.0	98.4	MEG_2725	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRB	NA
contig00005	138543	139733	EMRD	0/0	100.0	97.5	MEG_2729	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD	NA
contig00004	5697	6860	EMRK	0/0	100.0	97.4	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig00035	47420	47950	EMRR	0/0	100.0	98.5	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00004	4159	5697	EMRY	0/0	100.0	97.7	MEG_2736	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRY	NA
contig00020	72758	74401	EPTA	0/0	100.0	91.4	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig00004	7895	11488	EVGS	0/0	100.0	97.4	MEG_2869	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EVGS	NA
contig00008	188688	189416	GADW	0/0	100.0	100.0	MEG_3082	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig00008	189785	190609	GADX	0/0	100.0	93.9	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00025	39527	39940	HNS	0/0	100.0	99.3	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00001	42732	43404	KDPE	0/0	99.3	95.5	MEG_3448	Drugs:Aminoglycosides:Aminoglycoside_efflux_pumps:KDPE	NA
contig00002	289457	289846	MARA	0/0	100.0	99.0	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00002	289861	290295	MARR	0/0	100.0	98.2	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00011	29926	31158	MDFA	0/0	100.0	97.9	MEG_3737	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDFA	NA
contig00027	13300	14547	MDTA	0/0	100.0	95.6	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00027	14547	17669	MDTB	0/0	100.0	96.2	MEG_3747	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTB	NA
contig00027	17670	20747	MDTC	0/0	100.0	94.0	MEG_3749	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTC	NA
contig00008	184030	185187	MDTE	0/0	100.0	98.5	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00008	185212	188325	MDTF	0/0	100.0	97.3	MEG_3752	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTF	NA
contig00003	122019	123245	MDTG	0/0	100.0	98.5	MEG_3753	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig00003	112182	113390	MDTH	0/0	100.0	98.3	MEG_3755	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTH	NA
contig00002	258563	258892	MDTI	0/0	100.0	98.8	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00002	258211	258576	MDTJ	0/0	100.0	98.4	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00002	191249	192621	MDTK	0/0	99.9	97.7	MEG_3759	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:MDTK	NA
contig00030	38717	39949	MDTM	0/0	100.0	95.0	MEG_3761	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTM	NA
contig00020	42485	43516	MDTN	0/0	100.0	96.2	MEG_3763	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN	NA
contig00020	40434	42485	MDTO	0/0	100.0	97.0	MEG_3764	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTO	NA
contig00020	38971	40437	MDTP	0/0	100.0	97.6	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig00101	69	990	MPHA	1/1	100.0	99.7	MEG_4030	Drugs:MLS:Macrolide_phosphotransferases:MPHA	NA
contig00003	247892	249640	MSBA	0/0	100.0	98.1	MEG_4061	Drugs:Multi-drug_resistance:Multi-drug_ABC_efflux_pumps:MSBA	NA
contig00012	28735	29067	MVRC	0/0	100.0	92.2	MEG_4103	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MVRC	NA
contig00091	579	1409	OXA	0/0	100.0	100.0	MEG_4980	Drugs:betalactams:Class_D_betalactamases:OXA	NA
contig00001	101950	103851	PBP2	0/0	100.0	98.7	MEG_5400	Drugs:betalactams:Penicillin_binding_protein:PBP2	NA
contig00007	90060	91028	PMRF	0/0	100.0	97.6	MEG_5801	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF	NA
contig00010	19666	20535	ROBA	0/0	100.0	99.0	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00020	10618	10940	SOXS	0/0	99.7	98.1	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00062	2972	3939	SULI	0/0	100.0	100.0	MEG_6615	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULI	NA
contig00080	1723	2538	SULII	0/0	100.0	100.0	MEG_6617	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULII	NA
contig00050	15572	16817	TEM	0/0	98.3	99.4	MEG_6875	Drugs:betalactams:Class_A_betalactamases:TEM	NA
contig00078	914	2188	TETA	0/0	100.0	100.0	MEG_7024	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETA	NA
contig00034	39758	40924	UGD	0/0	100.0	96.0	MEG_7328	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:UGD	NA
contig00007	30212	31855	YOGI	0/0	100.0	97.4	MEG_7842	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:YOGI	NA

ID016I

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00348	167	1027	aac(3)-IId_1	0/0	100.0	99.9	EU022314	aac(3)-IId	Gentamicin, Tobramycin
contig00419	1539	2138	aac(6’)-Ib-cr_1	0/0	100.0	100.0	DQ303918	aac(6’)-Ib-cr	Ciprofloxacin
contig00286	2236	3037	aadA2_1	0/0	97.9	99.9	NC_010870	aadA2	Streptomycin
contig00008	62108	63253	blaCMY-76_1	0/0	100.0	99.0	JQ733573	blaCMY-76	Amoxicillin, Amoxicillin+Clavulanic_acid, Ampicillin, Ampicillin+Clavulanic_acid, Cefotaxime, Cefoxitin, Ceftazidime, Piperacillin, Piperacillin+Tazobactam, Ticarcillin, Ticarcillin+Clavulanic_acid
contig00395	1684	2559	blaCTX-M-15_1	0/0	100.0	100.0	AY044436	blaCTX-M-15	Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig00419	578	1408	blaOXA-1_1	0/0	100.0	100.0	HQ170510	blaOXA-1	Amoxicillin, Amoxicillin+Clavulanic_acid, Ampicillin, Ampicillin+Clavulanic_acid, Cefepime, Piperacillin, Piperacillin+Tazobactam
contig00184	5040	5900	blaTEM-1B_1	0/0	100.0	100.0	AY458016	blaTEM-1B	Amoxicillin, Ampicillin, Cephalothin, Piperacillin, Ticarcillin
contig00454	613	1256	catA1_1	0/0	97.6	99.8	V00622	catA1	Chloramphenicol
contig00286	1341	1838	dfrA12_8	0/0	100.0	100.0	AM040708	dfrA12	Trimethoprim
contig00005	4010	5242	mdf(A)_1	0/0	100.0	99.9	Y08743	mdf(A)
contig00471	68	989	mph(A)_2	1/1	100.0	99.7	U36578	mph(A)	Erythromycin, Azithromycin, Spiramycin, Telithromycin
contig00345	4316	4960	qnrB38_1	0/0	100.0	99.5	JN173060	qnrB38	Ciprofloxacin
contig00286	3515	4381	sul1_5	0/0	100.0	99.9	EU780013	sul1	Sulfamethoxazole
contig00380	1712	2958	tet(A)_6	0/0	97.8	100.0	AF534183	tet(A)	Doxycycline, Tetracycline

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00348	167	1027	AAC(3)-IId	0/0	100.0	99.9	EU022314.1:0-861	AAC(3)-IId is a plasmid-encoded aminoglycoside acetyltransferase in E. coli	aminoglycoside
contig00419	1539	2138	AAC(6’)-Ib-cr	0/0	100.0	100.0	DQ303918:0-600	AAC(6’)-Ib-cr is an aminoglycoside acetyltransferase encoded by plasmids transposons integrons in Enterobacteriaceae. The aac(6’)-Ib-cr variant gene can induce resistance against aminoglycoside and fluoroquinolone simultaneously	aminoglycoside, fluoroquinolone
contig00286	2258	3037	aadA2	0/0	100.0	99.9	AF156486:5012-5792	aadA2 is an aminoglycoside nucleotidyltransferase gene encoded by plasmids and integrons in K. pneumoniae Salmonella spp. Corynebacterium glutamicum C. freundii and Aeromonas spp.	aminoglycoside
contig00048	19781	22930	acrB	0/0	100.0	100.0	U00096.3:484403-481253	Protein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug/proton antiporter.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00022	38866	41979	acrD	0/0	100.0	100.0	AP009048.1:2586250-2589364	AcrD is an aminoglycoside efflux pump expressed in E. coli. Its expression can be induced by indole and is regulated by baeRS and cpxAR.	aminoglycoside
contig00260	8641	9798	acrE	0/0	100.0	99.9	U00096:3413863-3415021	AcrE is a membrane fusion protein similar to AcrA.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00260	5525	8629	acrF	0/0	100.0	99.9	U00096:3415032-3418137	AcrF is a inner membrane transporter similar to AcrB.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00260	10197	10859	acrS	0/0	100.0	100.0	U00096:3413465-3412802	AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.	cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00023	66950	67771	bacA	0/0	100.0	98.7	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00192	4385	5107	baeR	0/0	100.0	99.5	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00192	2985	4388	baeS	0/0	100.0	99.9	AP009048:2165012-2166416	BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.	aminocoumarin, aminoglycoside
contig00454	613	1256	catI	0/0	97.6	99.8	V00622:243-903	catI is a chromosome and transposon-encoded variant of the cat gene found in Escherichia coli and Acinetobacter baumannii	phenicol
contig00008	62108	63253	CMY-76	0/0	100.0	99.0	JQ733573:1027-2173	CMY-76 is a beta-lactamase. From the Lahey list of CMY beta-lactamases.	cephamycin
contig00079	28651	30024	cpxA	0/0	100.0	99.0	BA000007.3:4905062-4903688	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	aminocoumarin, aminoglycoside
contig00232	9608	10240	CRP	0/0	100.0	99.4	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00395	1684	2559	CTX-M-15	0/0	100.0	100.0	AY044436:1435-2311	CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family	cephalosporin
contig00286	1341	1838	dfrA12	0/0	100.0	100.0	GU585907.1:22103-21605	dfrA12 is an integron-encoded dihydrofolate reductase found in Vibrio cholerae	diaminopyrimidine
contig00116	22757	23929	emrA	0/0	100.0	100.0	AP009048:2810082-2811255	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	fluoroquinolone
contig00116	23946	25484	emrB	0/0	100.0	100.0	U00096:2812615-2814154	emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin.	fluoroquinolone
contig00162	10888	11943	emrK	0/0	100.0	99.9	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00116	22100	22630	emrR	0/0	100.0	99.8	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00162	9350	10888	emrY	0/0	100.0	99.9	D78168:1591-3130	emrY is a multidrug transport that moves substrates across the inner membrane of the Gram-negative E. coli. It is a homolog of emrB.	tetracycline
contig00131	7749	9392	eptA	0/0	100.0	99.9	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00048	22953	24146	Escherichia_coli_acrA	0/0	100.0	100.0	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00076	25623	26756	Escherichia_coli_ampC	0/0	100.0	97.3	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00205	3795	5099	Escherichia_coli_ampC1_beta-lactamase	0/0	100.0	99.9	FN649414.1:2765050-2766355	An ampC-like beta-lactamase identified from Escherichia coli.	cephalosporin, penam
contig00447	248	1366	Escherichia_coli_ampH	0/0	96.6	100.0	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig00005	4010	5242	Escherichia_coli_mdfA	0/0	100.0	98.4	JQ394987:0-1233	Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter.	benzalkonium_chloride, rhodamine, tetracycline
contig00162	12466	13080	evgA	0/0	100.0	100.0	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00162	13085	16678	evgS	0/0	100.0	100.0	U00096:2484373-2487967	EvgS is a sensor protein that phosphorylates the regulatory protein EvgA. evgS corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	fluoroquinolone, macrolide, penam, tetracycline
contig00343	1783	2511	gadW	0/0	100.0	94.7	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig00343	592	1416	gadX	0/0	100.0	100.0	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00150	17822	18235	H-NS	0/0	100.0	99.3	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00161	4873	5286	H-NS	0/0	100.0	90.8	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00166	8389	9066	kdpE	0/0	100.0	100.0	U00096.3:721733-721055	kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding.	aminoglycoside
contig00024	18240	18623	marA	0/0	100.0	100.0	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00329	4608	5855	mdtA	0/0	100.0	98.0	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00329	1486	4608	mdtB	0/0	100.0	99.8	U00096:2155262-2158385	MdtB is a transporter that forms a heteromultimer complex with MdtC to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex.	aminocoumarin
contig00095	747	1904	mdtE	0/0	100.0	100.0	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00033	18399	19625	mdtG	0/0	100.0	99.3	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00033	28254	29462	mdtH	0/0	100.0	100.0	U00096:1125326-1124117	Multidrug resistance protein MdtH	fluoroquinolone
contig00244	473	1684	mdtM	0/0	98.3	95.5	U00096.3:4568519-4567286	Multidrug resistance protein MdtM	acridine_dye, fluoroquinolone, lincosamide, nucleoside, phenicol
contig00209	10928	11959	mdtN	0/0	100.0	100.0	AP009048.1:4307588-4306556	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	acridine_dye, nucleoside
contig00209	11959	14010	mdtO	0/0	100.0	100.0	AP009048.1:4306557-4304505	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00209	14007	15473	mdtP	0/0	100.0	100.0	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00471	68	973	mphA	0/0	100.0	100.0	D16251.1:2531-1625	The mphA gene encodes for resistance enzyme MPH(2’)-I which preferentially inactivate 14-membered macrolides (e.g.erythromycin telithromycin roxithromycin) over 16-membered macrolides (e.g.tylosin spiramycin). It phosphorylates macrolides at 2’-OH hydroxyl of desosamine sugar of macrolides in a GTP-dependent manner.	macrolide
contig00022	17704	18180	mphB	0/0	100.0	98.3	AE005174.2:3397370-3397847	The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides.	macrolide
contig00005	86958	88706	msbA	0/0	100.0	100.0	U00096.3:966620-968369	MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability.	nitroimidazole
contig00419	578	1408	OXA-1	0/0	100.0	100.0	JN420336.1:2230-1399	OXA-1 is a beta-lactamase found in E. coli	cephalosporin, penam
contig00025	17666	18634	pmrF	0/0	100.0	100.0	U00096:2367070-2368039	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide
contig00345	4316	4960	QnrB38	0/0	100.0	99.5	JN173060:2306-2951	QnrB38 is a plasmid-mediated quinolone resistance protein found in Citrobacter freundii	fluoroquinolone
contig00286	3542	4381	sul1	0/0	100.0	100.0	JF969163:1053-1893	Sul1 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria. It is linked to other resistance genes of class 1 integrons.	sulfonamide
contig00184	5040	5900	TEM-1	0/0	100.0	99.9	AL513383:161910-162771	TEM-1 is a broad-spectrum beta-lactamase found in many Gram-negative bacteria. Confers resistance to penicillins and first generation cephalosphorins.	cephalosporin, monobactam, penam, penem
contig00380	1712	2958	tet(A)	0/0	97.8	100.0	AF534183.1:2970-4245	TetA is a tetracycline efflux pump found in many species of Gram-negative bacteria.	tetracycline
contig00023	43086	44573	tolC	0/0	100.0	99.7	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan
contig00059	42513	44156	yojI	0/0	100.0	100.0	U00096.3:2308615-2306971	YojI mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. YojI is capable of pumping out microcin molecules. The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI.	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00348	167	1027	(AGly)aac3-IId	0/0	100.0	99.9	EU022314:1-861	(AGly)aac3-IId	NA
contig00286	2258	3037	(AGly)aadA2	0/0	100.0	99.9	X68227:66-945	(AGly)aadA2	NA
contig00205	3795	5099	(Bla)AmpC1_Ecoli	0/0	100.0	99.9	FN649414:2765051-2766355	(Bla)AmpC1_Ecoli	NA
contig00076	25623	26756	(Bla)AmpC2_Ecoli	0/0	100.0	97.3	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00447	248	1366	(Bla)ampH_Ecoli	0/0	96.6	100.0	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00008	62108	63253	(Bla)blaCMY-76	0/0	100.0	99.0	JQ733573:1028-2173	(Bla)blaCMY-76	NA
contig00395	1684	2559	(Bla)blaCTX-M-15	0/0	100.0	100.0	JQ686199:261-1136	(Bla)blaCTX-M-15	NA
contig00419	578	1408	(Bla)blaOXA-1	0/0	100.0	100.0	JQ682867:1-831	(Bla)blaOXA-1	NA
contig00184	5040	5900	(Bla)blaTEM-105	0/0	100.0	99.9	AF516720:215-1075	(Bla)blaTEM-105	NA
contig00030	38587	40488	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100.0	100.0	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA
contig00345	4316	4960	(Flq)qnrB38	0/0	100.0	99.5	JN173060:2307-2951	(Flq)qnrB38	NA
contig00471	68	973	(MLS)mph(A)	0/0	100.0	100.0	DQ445270:1626-2531	(MLS)mph(A)	NA
contig00454	613	1256	(Phe)catA1	0/0	97.6	99.8	V00622:244-903	(Phe)catA1	NA
contig00286	3542	4381	(Sul)sul1	0/0	100.0	100.0	AF071413:6700-7539	(Sul)sul1	NA
contig00380	1684	2958	(Tet)tetA	0/0	100.0	100.0	JX424423:94438-95712	(Tet)tetA	NA
contig00286	1341	1838	(Tmt)dfrA12	0/0	100.0	100.0	Z21672:310-807	(Tmt)dfrA12	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00348	167	1027	aac(3)-IId	0/0	100.0	100.0	NG_047251.1	aminoglycoside N-acetyltransferase AAC(3)-IId	GENTAMICIN
contig00419	1539	2093	aac(6’)-Ib-D181Y	0/0	100.0	99.8	NG_067946.1	AAC(6’)-Ib family aminoglycoside 6’-N-acetyltransferase	AMIKACIN, KANAMYCIN, TOBRAMYCIN
contig00286	2246	3037	aadA2	0/0	100.0	100.0	NG_047343.1	ANT(3’’)-Ia family aminoglycoside nucleotidyltransferase AadA2	STREPTOMYCIN
contig00008	62108	63253	blaCMY-76	0/0	100.0	99.0	NG_048873.1	class C beta-lactamase CMY-76	CEPHALOSPORIN
contig00395	1684	2559	blaCTX-M-15	0/0	100.0	100.0	NG_048935.1	class A extended-spectrum beta-lactamase CTX-M-15	CEPHALOSPORIN
contig00076	25623	26756	blaEC-15	0/0	100.0	98.5	NG_049081.1	class C extended-spectrum beta-lactamase EC-15	CEPHALOSPORIN
contig00419	578	1408	blaOXA-1	0/0	100.0	100.0	NG_049392.1	oxacillin-hydrolyzing class D beta-lactamase OXA-1	CEPHALOSPORIN
contig00184	5040	5900	blaTEM-1	0/0	100.0	100.0	NG_050145.1	class A broad-spectrum beta-lactamase TEM-1	BETA-LACTAM
contig00454	613	1256	catA1	0/0	97.6	99.8	NG_047582.1	type A-1 chloramphenicol O-acetyltransferase	CHLORAMPHENICOL
contig00286	1341	1838	dfrA12	0/0	100.0	100.0	NG_047689.1	trimethoprim-resistant dihydrofolate reductase DfrA12	TRIMETHOPRIM
contig00471	68	989	mph(A)	1/1	100.0	99.7	NG_047986.1	Mph(A) family macrolide 2’-phosphotransferase	MACROLIDE
contig00345	4316	4960	qnrB38	0/0	100.0	99.5	NG_050500.1	quinolone resistance pentapeptide repeat protein QnrB38	QUINOLONE
contig00286	3542	4381	sul1	0/0	100.0	100.0	NG_048082.1	sulfonamide-resistant dihydropteroate synthase Sul1	SULFONAMIDE
contig00380	1684	2883	tet(A)	0/0	100.0	100.0	NG_048154.1	tetracycline efflux MFS transporter Tet(A)	TETRACYCLINE

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00348	167	1027	AAC3	0/0	100.0	100.0	MEG_64	Drugs:Aminoglycosides:Aminoglycoside_N-acetyltransferases:AAC3	NA
contig00048	22953	24146	ACRA	0/0	100.0	100.0	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00048	19781	22930	ACRB	0/0	100.0	100.0	MEG_401	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRB	NA
contig00022	38866	41979	ACRD	0/0	100.0	100.0	MEG_407	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ACRD	NA
contig00260	8641	9798	ACRE	0/0	100.0	99.9	MEG_408	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRE	NA
contig00260	5525	8629	ACRF	0/0	100.0	99.9	MEG_409	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRF	NA
contig00260	10197	10859	ACRS	0/0	100.0	100.0	MEG_415	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS	NA
contig00447	248	1366	AMPH	0/0	96.6	100.0	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00286	2236	3037	ANT3-DPRIME	0/0	97.9	99.9	MEG_975	Drugs:Aminoglycosides:Aminoglycoside_O-nucleotidyltransferases:ANT3-DPRIME	NA
contig00093	11915	13767	ASMA	0/0	100.0	97.2	MEG_1180	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:ASMA	NA
contig00023	66950	67771	BACA	0/0	100.0	98.9	MEG_1189	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00192	4385	5107	BAER	0/0	100.0	99.5	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00192	2985	4388	BAES	0/0	100.0	99.9	MEG_1193	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES	NA
contig00012	20589	21779	BCR	0/0	100.0	99.9	MEG_1210	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR	NA
contig00076	25623	26756	BLAEC	0/0	100.0	98.5	MEG_1282	Drugs:betalactams:Class_C_betalactamases:BLAEC	NA
contig00454	613	1256	CATA	0/0	97.6	100.0	MEG_1584	Drugs:Phenicol:Chloramphenicol_acetyltransferases:CATA	NA
contig00008	61101	61976	CMY	0/0	100.0	94.2	MEG_1992	Drugs:betalactams:Class_C_betalactamases:CMY	NA
contig00008	62045	63270	CMY	0/0	100.0	98.4	MEG_1955	Drugs:betalactams:Class_C_betalactamases:CMY	NA
contig00079	27956	28654	CPXAR	0/0	100.0	100.0	MEG_2122	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00079	28651	30024	CPXAR	0/0	100.0	100.0	MEG_2121	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00232	9608	10240	CRP	0/0	100.0	99.4	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00286	1341	1838	DFRA	0/0	100.0	100.0	MEG_2551	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00116	22757	23929	EMRA	0/0	100.0	100.0	MEG_2722	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA	NA
contig00116	23946	25484	EMRB	0/0	100.0	100.0	MEG_2725	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRB	NA
contig00003	87250	88440	EMRD	0/0	100.0	100.0	MEG_2729	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD	NA
contig00162	10888	12051	EMRK	0/0	100.0	99.9	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig00116	22100	22630	EMRR	0/0	100.0	99.8	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00162	9350	10888	EMRY	0/0	100.0	99.9	MEG_2736	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRY	NA
contig00131	7749	9392	EPTA	0/0	100.0	99.9	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig00162	13085	16678	EVGS	0/0	100.0	100.0	MEG_2870	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EVGS	NA
contig00343	1783	2511	GADW	0/0	100.0	100.0	MEG_3081	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig00343	592	1416	GADX	0/0	100.0	100.0	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00150	17822	18235	HNS	0/0	100.0	99.3	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00161	4873	5286	HNS	0/0	100.0	90.8	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00166	8389	9066	KDPE	0/0	100.0	100.0	MEG_3448	Drugs:Aminoglycosides:Aminoglycoside_efflux_pumps:KDPE	NA
contig00024	18234	18623	MARA	0/0	100.0	100.0	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00024	17786	18220	MARR	0/0	100.0	100.0	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00005	4010	5242	MDFA	0/0	100.0	100.0	MEG_3737	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDFA	NA
contig00329	4608	5855	MDTA	0/0	100.0	98.0	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00329	1486	4608	MDTB	0/0	100.0	99.8	MEG_3747	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTB	NA
contig00095	747	1904	MDTE	0/0	100.0	100.0	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00033	18399	19625	MDTG	0/0	100.0	99.9	MEG_3753	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig00033	28254	29462	MDTH	0/0	100.0	100.0	MEG_3755	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTH	NA
contig00024	51016	51345	MDTI	0/0	100.0	100.0	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00024	51332	51697	MDTJ	0/0	100.0	99.5	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00011	37583	38956	MDTK	0/0	100.0	100.0	MEG_3759	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:MDTK	NA
contig00244	473	1684	MDTM	0/0	98.3	95.5	MEG_3761	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTM	NA
contig00209	10928	11959	MDTN	0/0	100.0	100.0	MEG_3763	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN	NA
contig00209	11959	14010	MDTO	0/0	100.0	100.0	MEG_3764	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTO	NA
contig00209	14007	15473	MDTP	0/0	100.0	100.0	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig00471	68	989	MPHA	1/1	100.0	99.7	MEG_4030	Drugs:MLS:Macrolide_phosphotransferases:MPHA	NA
contig00022	17704	18180	MPHB	0/0	100.0	98.3	MEG_4033	Drugs:MLS:Macrolide_phosphotransferases:MPHB	NA
contig00005	86958	88706	MSBA	0/0	100.0	100.0	MEG_4061	Drugs:Multi-drug_resistance:Multi-drug_ABC_efflux_pumps:MSBA	NA
contig00419	578	1408	OXA	0/0	100.0	100.0	MEG_4980	Drugs:betalactams:Class_D_betalactamases:OXA	NA
contig00030	38587	40488	PBP2	0/0	100.0	100.0	MEG_5400	Drugs:betalactams:Penicillin_binding_protein:PBP2	NA
contig00205	3795	5099	PBP4B	0/0	100.0	99.9	MEG_5409	Drugs:betalactams:Penicillin_binding_protein:PBP4B	NA
contig00025	17666	18634	PMRF	0/0	100.0	100.0	MEG_5801	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF	NA
contig00345	4316	4960	QNRB	0/0	100.0	99.5	MEG_5926	Drugs:Fluoroquinolones:Quinolone_resistance_protein_Qnr:QNRB	NA
contig00073	19983	20852	ROBA	0/0	100.0	99.0	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00091	21006	21329	SOXS	0/0	100.0	100.0	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00286	3541	4508	SULI	0/0	100.0	100.0	MEG_6615	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULI	NA
contig00184	4673	5918	TEM	0/0	98.3	99.4	MEG_6875	Drugs:betalactams:Class_A_betalactamases:TEM	NA
contig00380	1684	2958	TETA	0/0	100.0	100.0	MEG_7024	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETA	NA
contig00425	1543	1959	TETD	0/0	100.0	100.0	MEG_7070	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETD	NA
contig00059	42513	44156	YOGI	0/0	100.0	100.0	MEG_7842	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:YOGI	NA

ID017

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00002	231391	232266	blaCTX-M-15_1	0/0	100	100.0	AY044436	blaCTX-M-15	Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig00018	26130	27362	mdf(A)_1	0/0	100	99.1	Y08743	mdf(A)
contig00002	226094	226750	qnrS1_1	0/0	100	100.0	AB187515	qnrS1	Ciprofloxacin

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00010	124682	127831	acrB	0/0	100.0	99.1	U00096.3:484403-481253	Protein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug/proton antiporter.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00006	117709	120822	acrD	0/0	100.0	98.8	AP009048.1:2586250-2589364	AcrD is an aminoglycoside efflux pump expressed in E. coli. Its expression can be induced by indole and is regulated by baeRS and cpxAR.	aminoglycoside
contig00004	270325	271482	acrE	0/0	100.0	99.0	U00096:3413863-3415021	AcrE is a membrane fusion protein similar to AcrA.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00004	271494	274598	acrF	0/0	100.0	99.0	U00096:3415032-3418137	AcrF is a inner membrane transporter similar to AcrB.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00004	269264	269926	acrS	0/0	100.0	98.6	U00096:3413465-3412802	AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.	cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00004	60021	60840	bacA	0/0	99.8	98.7	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00002	277506	278228	baeR	0/0	100.0	99.5	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00002	278225	279628	baeS	0/0	100.0	98.7	AP009048:2165012-2166416	BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.	aminocoumarin, aminoglycoside
contig00025	22569	23942	cpxA	0/0	100.0	98.5	BA000007.3:4905062-4903688	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	aminocoumarin, aminoglycoside
contig00008	15235	15867	CRP	0/0	100.0	99.2	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00002	231391	232266	CTX-M-15	0/0	100.0	100.0	AY044436:1435-2311	CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family	cephalosporin
contig00005	27204	28376	emrA	0/0	100.0	98.2	AP009048:2810082-2811255	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	fluoroquinolone
contig00005	28393	29931	emrB	0/0	100.0	98.5	U00096:2812615-2814154	emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin.	fluoroquinolone
contig00006	25955	27010	emrK	0/0	100.0	98.7	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00005	26547	27077	emrR	0/0	100.0	100.0	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00006	24417	25955	emrY	0/0	100.0	98.8	D78168:1591-3130	emrY is a multidrug transport that moves substrates across the inner membrane of the Gram-negative E. coli. It is a homolog of emrB.	tetracycline
contig00011	115182	116825	eptA	0/0	100.0	99.2	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00010	127854	129047	Escherichia_coli_acrA	0/0	100.0	99.8	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00021	50255	51388	Escherichia_coli_ampC	0/0	100.0	97.2	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00006	85287	86591	Escherichia_coli_ampC1_beta-lactamase	0/0	100.0	98.2	FN649414.1:2765050-2766355	An ampC-like beta-lactamase identified from Escherichia coli.	cephalosporin, penam
contig00010	36338	37495	Escherichia_coli_ampH	0/0	100.0	98.7	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig00009	136225	136557	Escherichia_coli_emrE	0/0	100.0	92.2	Z11877.1:485-818	Member of the small MDR (multidrug resistance) family of transporters, in Escherichia coli this protein provides resistance against a number of positively charged compounds including ethidium bromide and erythromycin, proton-dependent secondary transporter which exchanges protons for compound translocation	macrolide
contig00018	26130	27362	Escherichia_coli_mdfA	0/0	100.0	97.6	JQ394987:0-1233	Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter.	benzalkonium_chloride, rhodamine, tetracycline
contig00006	27534	28148	evgA	0/0	100.0	99.0	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00006	28153	31746	evgS	0/0	100.0	99.5	U00096:2484373-2487967	EvgS is a sensor protein that phosphorylates the regulatory protein EvgA. evgS corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	fluoroquinolone, macrolide, penam, tetracycline
contig00008	190353	191081	gadW	0/0	100.0	94.4	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig00008	191449	192273	gadX	0/0	100.0	97.8	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00001	252998	253411	H-NS	0/0	100.0	99.3	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00012	8273	8945	kdpE	0/0	99.3	97.2	U00096.3:721733-721055	kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding.	aminoglycoside
contig00003	245056	245439	marA	0/0	100.0	99.5	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00002	287241	288488	mdtA	0/0	100.0	98.2	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00002	284119	287241	mdtB	0/0	100.0	98.0	U00096:2155262-2158385	MdtB is a transporter that forms a heteromultimer complex with MdtC to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex.	aminocoumarin
contig00002	281041	284118	mdtC	0/0	100.0	98.1	U00096:2158385-2161463	MdtC is a transporter that forms a heteromultimer complex with MdtB to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex. In the absence of MdtB MdtC can form a homomultimer complex that results in a functioning efflux complex with a narrower drug specificity. mdtC corresponds to 3 loci in Pseudomonas aeruginosa PAO1 (gene name: muxC/muxB) and 3 loci in Pseudomonas aeruginosa LESB58.	aminocoumarin
contig00008	185695	186852	mdtE	0/0	100.0	99.7	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00008	186877	189990	mdtF	0/0	100.0	98.6	U00096:3660413-3663527	MdtF is the multidrug inner membrane transporter for the MdtEF-TolC efflux complex.	fluoroquinolone, macrolide, penam
contig00001	462445	463671	mdtG	0/0	100.0	99.2	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00001	452606	453814	mdtH	0/0	100.0	98.8	U00096:1125326-1124117	Multidrug resistance protein MdtH	fluoroquinolone
contig00011	91422	92453	mdtN	0/0	100.0	98.0	AP009048.1:4307588-4306556	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	acridine_dye, nucleoside
contig00011	89371	91422	mdtO	0/0	100.0	98.8	AP009048.1:4306557-4304505	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00011	87908	89374	mdtP	0/0	100.0	98.2	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00006	142312	142788	mphB	0/0	100.0	98.3	AE005174.2:3397370-3397847	The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides.	macrolide
contig00001	598759	600507	msbA	0/0	100.0	99.0	U00096.3:966620-968369	MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability.	nitroimidazole
contig00002	76806	77774	pmrF	0/0	100.0	99.3	U00096:2367070-2368039	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide
contig00002	226094	226750	QnrS1	0/0	100.0	100.0	DQ485529.1:0-657	QnrS1 is a plasmid-mediated quinolone resistance protein found in Shigella flexneri	fluoroquinolone
contig00004	36175	37662	tolC	0/0	100.0	98.4	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan
contig00026	37105	38271	ugd	0/0	100.0	95.9	U00096:2099613-2098446	PmrE is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin	peptide
contig00002	124793	126436	yojI	0/0	100.0	98.2	U00096.3:2308615-2306971	YojI mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. YojI is capable of pumping out microcin molecules. The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI.	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00006	85287	86591	(Bla)AmpC1_Ecoli	0/0	100	98.2	FN649414:2765051-2766355	(Bla)AmpC1_Ecoli	NA
contig00021	50255	51388	(Bla)AmpC2_Ecoli	0/0	100	97.2	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00010	36338	37495	(Bla)ampH_Ecoli	0/0	100	98.7	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00002	231391	232266	(Bla)blaCTX-M-15	0/0	100	100.0	JQ686199:261-1136	(Bla)blaCTX-M-15	NA
contig00012	60734	62635	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100	98.7	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA
contig00002	226094	226750	(Flq)qnr-S1	0/0	100	100.0	AB187515:9737-10393	(Flq)qnr-S1	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00002	231391	232266	blaCTX-M-15	0/0	100	100.0	NG_048935.1	class A extended-spectrum beta-lactamase CTX-M-15	CEPHALOSPORIN
contig00021	50255	51388	blaEC-13	0/0	100	99.6	NG_049079.1	class C extended-spectrum beta-lactamase EC-13	CEPHALOSPORIN
contig00002	226094	226750	qnrS1	0/0	100	100.0	NG_050543.1	quinolone resistance pentapeptide repeat protein QnrS1	QUINOLONE

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00010	127854	129047	ACRA	0/0	100.0	99.8	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00010	124682	127831	ACRB	0/0	100.0	99.1	MEG_401	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRB	NA
contig00006	117709	120822	ACRD	0/0	100.0	98.8	MEG_407	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ACRD	NA
contig00004	270325	271482	ACRE	0/0	100.0	99.0	MEG_408	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRE	NA
contig00004	271494	274598	ACRF	0/0	100.0	99.0	MEG_409	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRF	NA
contig00004	269264	269926	ACRS	0/0	100.0	98.6	MEG_415	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS	NA
contig00010	36338	37495	AMPH	0/0	100.0	98.7	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00002	300095	301947	ASMA	0/0	100.0	98.1	MEG_1180	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:ASMA	NA
contig00004	60021	60840	BACA	0/0	99.8	98.9	MEG_1189	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00002	277506	278228	BAER	0/0	100.0	99.5	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00002	278225	279628	BAES	0/0	100.0	98.7	MEG_1193	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES	NA
contig00002	151708	152898	BCR	0/0	100.0	98.2	MEG_1210	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR	NA
contig00021	50255	51388	BLAEC	0/0	100.0	99.6	MEG_1280	Drugs:betalactams:Class_C_betalactamases:BLAEC	NA
contig00025	21874	22572	CPXAR	0/0	100.0	99.4	MEG_2118	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00025	22569	23942	CPXAR	0/0	100.0	99.1	MEG_2121	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00008	15235	15867	CRP	0/0	100.0	99.2	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00005	27204	28376	EMRA	0/0	100.0	98.2	MEG_2722	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA	NA
contig00005	28393	29931	EMRB	0/0	100.0	98.5	MEG_2725	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRB	NA
contig00015	27098	28288	EMRD	0/0	100.0	99.9	MEG_2729	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD	NA
contig00006	25955	27118	EMRK	0/0	100.0	98.8	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig00005	26547	27077	EMRR	0/0	100.0	100.0	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00006	24417	25955	EMRY	0/0	100.0	98.9	MEG_2736	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRY	NA
contig00011	115182	116825	EPTA	0/0	100.0	99.2	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig00006	28153	31746	EVGS	0/0	100.0	99.5	MEG_2870	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EVGS	NA
contig00008	190353	191081	GADW	0/0	100.0	98.6	MEG_3081	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig00008	191449	192273	GADX	0/0	100.0	97.8	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00001	252998	253411	HNS	0/0	100.0	99.3	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00012	8273	8945	KDPE	0/0	99.3	97.2	MEG_3448	Drugs:Aminoglycosides:Aminoglycoside_efflux_pumps:KDPE	NA
contig00003	245056	245445	MARA	0/0	100.0	99.5	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00003	245459	245893	MARR	0/0	100.0	97.7	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00018	26130	27362	MDFA	0/0	100.0	99.2	MEG_3737	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDFA	NA
contig00002	287241	288488	MDTA	0/0	100.0	98.2	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00002	284119	287241	MDTB	0/0	100.0	98.0	MEG_3747	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTB	NA
contig00002	281041	284118	MDTC	0/0	100.0	98.1	MEG_3749	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTC	NA
contig00008	185695	186852	MDTE	0/0	100.0	99.7	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00008	186877	189990	MDTF	0/0	100.0	98.6	MEG_3752	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTF	NA
contig00001	462445	463671	MDTG	0/0	100.0	99.3	MEG_3753	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig00001	452606	453814	MDTH	0/0	100.0	98.8	MEG_3755	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTH	NA
contig00003	206081	206410	MDTI	0/0	100.0	99.7	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00003	205729	206094	MDTJ	0/0	100.0	98.9	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00003	134591	135964	MDTK	0/0	100.0	99.0	MEG_3759	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:MDTK	NA
contig00011	91422	92453	MDTN	0/0	100.0	98.0	MEG_3763	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN	NA
contig00011	89371	91422	MDTO	0/0	100.0	98.8	MEG_3764	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTO	NA
contig00011	87908	89374	MDTP	0/0	100.0	98.2	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig00006	142312	142788	MPHB	0/0	100.0	98.3	MEG_4033	Drugs:MLS:Macrolide_phosphotransferases:MPHB	NA
contig00001	598759	600507	MSBA	0/0	100.0	99.0	MEG_4061	Drugs:Multi-drug_resistance:Multi-drug_ABC_efflux_pumps:MSBA	NA
contig00009	136225	136557	MVRC	0/0	100.0	92.2	MEG_4103	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MVRC	NA
contig00012	60734	62635	PBP2	0/0	100.0	98.7	MEG_5400	Drugs:betalactams:Penicillin_binding_protein:PBP2	NA
contig00006	85287	86591	PBP4B	0/0	100.0	98.2	MEG_5409	Drugs:betalactams:Penicillin_binding_protein:PBP4B	NA
contig00002	76806	77774	PMRF	0/0	100.0	99.3	MEG_5801	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF	NA
contig00002	226094	226750	QNRS	0/0	100.0	100.0	MEG_6020	Drugs:Fluoroquinolones:Quinolone_resistance_protein_Qnr:QNRS	NA
contig00013	11905	12774	ROBA	0/0	100.0	99.1	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00011	65969	66291	SOXS	0/0	99.7	99.7	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00026	37105	38271	UGD	0/0	100.0	95.9	MEG_7328	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:UGD	NA
contig00002	124793	126436	YOGI	0/0	100.0	98.2	MEG_7842	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:YOGI	NA

ID018CT

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00086	5283	6086	aph(3’’)-Ib_5	0/0	100	99.9	AF321551	aph(3’’)-Ib	Streptomycin
contig00086	4447	5283	aph(6)-Id_1	0/0	100	99.9	M28829	aph(6)-Id	Streptomycin
contig00090	7643	8518	blaCTX-M-27_1	0/0	100	100.0	AY156923	blaCTX-M-27	Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig00086	3356	4216	blaTEM-1B_1	0/0	100	100.0	AY458016	blaTEM-1B	Amoxicillin, Ampicillin, Cephalothin, Piperacillin, Ticarcillin
contig00151	4	486	dfrA14_5	0/0	100	99.6	DQ388123	dfrA14	Trimethoprim
contig00014	5710	6942	mdf(A)_1	0/0	100	98.9	Y08743	mdf(A)
contig00142	68	989	mph(A)_2	1/1	100	99.7	U36578	mph(A)	Erythromycin, Azithromycin, Spiramycin, Telithromycin
contig00086	6147	6962	sul2_2	0/0	100	100.0	AY034138	sul2	Sulfamethoxazole

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00001	38814	41963	acrB	0/0	100.0	99.6	U00096.3:484403-481253	Protein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug/proton antiporter.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00002	138982	142095	acrD	0/0	100.0	99.3	AP009048.1:2586250-2589364	AcrD is an aminoglycoside efflux pump expressed in E. coli. Its expression can be induced by indole and is regulated by baeRS and cpxAR.	aminoglycoside
contig00004	124199	125356	acrE	0/0	100.0	99.7	U00096:3413863-3415021	AcrE is a membrane fusion protein similar to AcrA.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00004	125368	128472	acrF	0/0	100.0	99.5	U00096:3415032-3418137	AcrF is a inner membrane transporter similar to AcrB.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00004	123138	123800	acrS	0/0	100.0	99.1	U00096:3413465-3412802	AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.	cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00086	5283	6086	APH(3’’)-Ib	0/0	100.0	99.6	AF313472:15593-16397	APH(3’’)-Ib is an aminoglycoside phosphotransferase encoded by plasmids transposons integrative conjugative elements and chromosomes in Enterobacteriaceae and Pseudomonas spp.	aminoglycoside
contig00086	4447	5283	APH(6)-Id	0/0	100.0	99.8	AF024602:3155-3992	APH(6)-Id is an aminoglycoside phosphotransferase encoded by plasmids integrative conjugative elements and chromosomal genomic islands in K. pneumoniae Salmonella spp. E. coli Shigella flexneri Providencia alcalifaciens Pseudomonas spp. V. cholerae Edwardsiella tarda Pasteurella multocida and Aeromonas bestiarum	aminoglycoside
contig00007	89770	90591	bacA	0/0	100.0	100.0	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00011	31718	32440	baeR	0/0	100.0	100.0	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00011	32437	33840	baeS	0/0	100.0	100.0	AP009048:2165012-2166416	BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.	aminocoumarin, aminoglycoside
contig00019	61378	62751	cpxA	0/0	100.0	99.0	BA000007.3:4905062-4903688	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	aminocoumarin, aminoglycoside
contig00012	15387	16019	CRP	0/0	100.0	99.8	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00090	7643	8518	CTX-M-27	0/0	100.0	100.0	AY156923:0-876	CTX-M-27 is a beta-lactamase found in Escherichia coli	cephalosporin
contig00151	4	486	dfrA14	0/0	100.0	99.8	EU780012:2162-2645	dfrA14 is an integron-encoded dihydrofolate reductase found in Escherichia coli	diaminopyrimidine
contig00006	23419	24591	emrA	0/0	100.0	98.1	AP009048:2810082-2811255	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	fluoroquinolone
contig00006	24608	26146	emrB	0/0	100.0	99.3	U00096:2812615-2814154	emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin.	fluoroquinolone
contig00009	95966	97021	emrK	0/0	100.0	99.9	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00006	22762	23292	emrR	0/0	100.0	100.0	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00009	94428	95966	emrY	0/0	100.0	99.0	D78168:1591-3130	emrY is a multidrug transport that moves substrates across the inner membrane of the Gram-negative E. coli. It is a homolog of emrB.	tetracycline
contig00003	168410	170053	eptA	0/0	100.0	99.9	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00001	37598	38791	Escherichia_coli_acrA	0/0	100.0	99.8	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00003	125058	126191	Escherichia_coli_ampC	0/0	100.0	98.5	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00002	170322	171626	Escherichia_coli_ampC1_beta-lactamase	0/0	100.0	99.7	FN649414.1:2765050-2766355	An ampC-like beta-lactamase identified from Escherichia coli.	cephalosporin, penam
contig00001	126930	128087	Escherichia_coli_ampH	0/0	100.0	99.9	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig00037	15236	15568	Escherichia_coli_emrE	0/0	100.0	100.0	Z11877.1:485-818	Member of the small MDR (multidrug resistance) family of transporters, in Escherichia coli this protein provides resistance against a number of positively charged compounds including ethidium bromide and erythromycin, proton-dependent secondary transporter which exchanges protons for compound translocation	macrolide
contig00014	5710	6942	Escherichia_coli_mdfA	0/0	100.0	97.3	JQ394987:0-1233	Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter.	benzalkonium_chloride, rhodamine, tetracycline
contig00009	97545	98159	evgA	0/0	100.0	100.0	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00009	98164	101757	evgS	0/0	100.0	99.7	U00096:2484373-2487967	EvgS is a sensor protein that phosphorylates the regulatory protein EvgA. evgS corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	fluoroquinolone, macrolide, penam, tetracycline
contig00058	1784	2512	gadW	0/0	100.0	94.7	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig00058	592	1416	gadX	0/0	100.0	99.9	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00062	21689	22102	H-NS	0/0	100.0	99.3	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00066	8452	9129	kdpE	0/0	100.0	100.0	U00096.3:721733-721055	kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding.	aminoglycoside
contig00033	31082	31465	marA	0/0	100.0	99.7	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00011	41453	42700	mdtA	0/0	100.0	97.5	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00011	38331	41453	mdtB	0/0	100.0	98.8	U00096:2155262-2158385	MdtB is a transporter that forms a heteromultimer complex with MdtC to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex.	aminocoumarin
contig00011	35253	38330	mdtC	0/0	100.0	99.8	U00096:2158385-2161463	MdtC is a transporter that forms a heteromultimer complex with MdtB to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex. In the absence of MdtB MdtC can form a homomultimer complex that results in a functioning efflux complex with a narrower drug specificity. mdtC corresponds to 3 loci in Pseudomonas aeruginosa PAO1 (gene name: muxC/muxB) and 3 loci in Pseudomonas aeruginosa LESB58.	aminocoumarin
contig00058	6013	7170	mdtE	0/0	100.0	100.0	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00058	2875	5988	mdtF	0/0	100.0	99.9	U00096:3660413-3663527	MdtF is the multidrug inner membrane transporter for the MdtEF-TolC efflux complex.	fluoroquinolone, macrolide, penam
contig00010	89535	90761	mdtG	0/0	100.0	99.3	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00010	79697	80905	mdtH	0/0	100.0	97.8	U00096:1125326-1124117	Multidrug resistance protein MdtH	fluoroquinolone
contig00024	35501	36712	mdtM	0/0	98.3	95.9	U00096.3:4568519-4567286	Multidrug resistance protein MdtM	acridine_dye, fluoroquinolone, lincosamide, nucleoside, phenicol
contig00045	34133	35164	mdtN	0/0	100.0	99.9	AP009048.1:4307588-4306556	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	acridine_dye, nucleoside
contig00045	32082	34133	mdtO	0/0	100.0	100.0	AP009048.1:4306557-4304505	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00045	30619	32085	mdtP	0/0	100.0	98.1	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00142	68	973	mphA	0/0	100.0	100.0	D16251.1:2531-1625	The mphA gene encodes for resistance enzyme MPH(2’)-I which preferentially inactivate 14-membered macrolides (e.g.erythromycin telithromycin roxithromycin) over 16-membered macrolides (e.g.tylosin spiramycin). It phosphorylates macrolides at 2’-OH hydroxyl of desosamine sugar of macrolides in a GTP-dependent manner.	macrolide
contig00002	117826	118302	mphB	0/0	100.0	98.3	AE005174.2:3397370-3397847	The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides.	macrolide
contig00020	40795	42543	msbA	0/0	100.0	100.0	U00096.3:966620-968369	MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability.	nitroimidazole
contig00044	22851	23819	pmrF	0/0	100.0	100.0	U00096:2367070-2368039	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide
contig00086	6147	6962	sul2	0/0	100.0	100.0	AY055428.1:21084-20268	Sul2 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria usually found on small plasmids.	sulfonamide
contig00086	3356	4216	TEM-1	0/0	100.0	99.9	AL513383:161910-162771	TEM-1 is a broad-spectrum beta-lactamase found in many Gram-negative bacteria. Confers resistance to penicillins and first generation cephalosphorins.	cephalosporin, monobactam, penam, penem
contig00007	65905	67392	tolC	0/0	100.0	99.9	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan
contig00043	35270	36913	yojI	0/0	100.0	98.2	U00096.3:2308615-2306971	YojI mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. YojI is capable of pumping out microcin molecules. The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI.	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00086	5283	6086	(AGly)strA	0/0	100	99.8	AB366441:22458-23261	(AGly)strA	NA
contig00086	4447	5283	(AGly)strB	0/0	100	99.9	FJ474091:264-1100	(AGly)strB	NA
contig00002	170322	171626	(Bla)AmpC1_Ecoli	0/0	100	99.7	FN649414:2765051-2766355	(Bla)AmpC1_Ecoli	NA
contig00003	125058	126191	(Bla)AmpC2_Ecoli	0/0	100	98.5	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00001	126930	128087	(Bla)ampH_Ecoli	0/0	100	99.9	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00090	7643	8518	(Bla)blaCTX-M-27	0/0	100	100.0	AY156923:1-876	(Bla)blaCTX-M-27	NA
contig00086	3356	4216	(Bla)blaTEM-105	0/0	100	99.9	AF516720:215-1075	(Bla)blaTEM-105	NA
contig00021	10335	12236	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100	100.0	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA
contig00142	68	973	(MLS)mph(A)	0/0	100	100.0	DQ445270:1626-2531	(MLS)mph(A)	NA
contig00086	6147	6962	(Sul)sul2	0/0	100	100.0	EU360945:1617-2432	(Sul)sul2	NA
contig00151	4	477	(Tmt)dfrA14	0/0	100	100.0	GU726917:72-545	(Tmt)dfrA14	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00086	5283	6110	aph(3’’)-Ib	0/0	100	99.9	NG_056002.2	aminoglycoside O-phosphotransferase APH(3’’)-Ib	STREPTOMYCIN
contig00086	4447	5283	aph(6)-Id	0/0	100	100.0	NG_047466.1	aminoglycoside O-phosphotransferase APH(6)-Id	STREPTOMYCIN
contig00090	7643	8518	blaCTX-M-27	0/0	100	100.0	NG_048976.1	class A extended-spectrum beta-lactamase CTX-M-27	CEPHALOSPORIN
contig00003	125058	126191	blaEC	0/0	100	100.0	NG_047496.1	BlaEC family class C beta-lactamase	BETA-LACTAM
contig00086	3356	4216	blaTEM-1	0/0	100	100.0	NG_050145.1	class A broad-spectrum beta-lactamase TEM-1	BETA-LACTAM
contig00151	4	477	dfrA14	0/0	100	100.0	NG_056035.1	trimethoprim-resistant dihydrofolate reductase DfrA14	TRIMETHOPRIM
contig00142	68	989	mph(A)	1/1	100	99.7	NG_047986.1	Mph(A) family macrolide 2’-phosphotransferase	MACROLIDE
contig00086	6147	6962	sul2	0/0	100	100.0	NG_051852.1	sulfonamide-resistant dihydropteroate synthase Sul2	SULFONAMIDE

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00001	37598	38791	ACRA	0/0	100.0	99.8	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00001	38814	41963	ACRB	0/0	100.0	99.6	MEG_401	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRB	NA
contig00002	138982	142095	ACRD	0/0	100.0	99.3	MEG_407	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ACRD	NA
contig00004	124199	125356	ACRE	0/0	100.0	99.7	MEG_408	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRE	NA
contig00004	125368	128472	ACRF	0/0	100.0	99.5	MEG_409	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRF	NA
contig00004	123138	123800	ACRS	0/0	100.0	99.1	MEG_415	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS	NA
contig00001	126930	128087	AMPH	0/0	100.0	99.9	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00086	5283	6110	APH3-DPRIME	0/0	100.0	99.9	MEG_1019	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH3-DPRIME	NA
contig00086	4447	5283	APH6	0/0	100.0	100.0	MEG_1084	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH6	NA
contig00011	55019	56871	ASMA	0/0	100.0	98.2	MEG_1180	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:ASMA	NA
contig00007	89770	90591	BACA	0/0	100.0	100.0	MEG_1190	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00011	31718	32440	BAER	0/0	100.0	100.0	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00011	32437	33840	BAES	0/0	100.0	100.0	MEG_1193	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES	NA
contig00018	49268	50458	BCR	0/0	100.0	100.0	MEG_1210	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR	NA
contig00003	125058	126191	BLAEC	0/0	100.0	100.0	MEG_1276	Drugs:betalactams:Class_C_betalactamases:BLAEC	NA
contig00019	60683	61381	CPXAR	0/0	100.0	99.9	MEG_2122	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00019	61378	62751	CPXAR	0/0	100.0	99.7	MEG_2121	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00012	15387	16019	CRP	0/0	100.0	99.8	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00090	6666	7608	CTX	0/0	100.0	100.0	MEG_2435	Drugs:betalactams:Class_A_betalactamases:CTX	NA
contig00090	7637	8540	CTX	0/0	100.0	99.8	MEG_2401	Drugs:betalactams:Class_A_betalactamases:CTX	NA
contig00151	4	477	DFRA	0/0	100.0	99.8	MEG_2517	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00006	23419	24591	EMRA	0/0	100.0	98.1	MEG_2722	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA	NA
contig00006	24608	26146	EMRB	0/0	100.0	99.3	MEG_2725	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRB	NA
contig00067	16031	17221	EMRD	0/0	100.0	100.0	MEG_2729	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD	NA
contig00009	95966	97129	EMRK	0/0	100.0	99.9	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig00006	22762	23292	EMRR	0/0	100.0	100.0	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00009	94428	95966	EMRY	0/0	100.0	99.1	MEG_2736	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRY	NA
contig00003	168410	170053	EPTA	0/0	100.0	99.9	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig00009	98164	101757	EVGS	0/0	100.0	99.7	MEG_2870	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EVGS	NA
contig00058	1784	2512	GADW	0/0	100.0	100.0	MEG_3081	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig00058	592	1416	GADX	0/0	100.0	99.9	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00062	21689	22102	HNS	0/0	100.0	99.3	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00066	8452	9129	KDPE	0/0	100.0	100.0	MEG_3448	Drugs:Aminoglycosides:Aminoglycoside_efflux_pumps:KDPE	NA
contig00033	31076	31465	MARA	0/0	100.0	99.7	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00033	30627	31061	MARR	0/0	100.0	98.4	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00014	5710	6942	MDFA	0/0	100.0	99.0	MEG_3737	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDFA	NA
contig00011	41453	42700	MDTA	0/0	100.0	97.5	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00011	38331	41453	MDTB	0/0	100.0	98.8	MEG_3747	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTB	NA
contig00011	35253	38330	MDTC	0/0	100.0	99.8	MEG_3749	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTC	NA
contig00058	6013	7170	MDTE	0/0	100.0	100.0	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00058	2875	5988	MDTF	0/0	100.0	99.9	MEG_3752	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTF	NA
contig00010	89535	90761	MDTG	0/0	100.0	99.9	MEG_3753	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig00010	79697	80905	MDTH	0/0	100.0	97.8	MEG_3755	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTH	NA
contig00042	19225	19554	MDTI	0/0	100.0	100.0	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00042	19541	19906	MDTJ	0/0	100.0	99.5	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00016	26404	27777	MDTK	0/0	100.0	98.8	MEG_3759	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:MDTK	NA
contig00024	35501	36712	MDTM	0/0	98.3	95.9	MEG_3761	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTM	NA
contig00045	34133	35164	MDTN	0/0	100.0	99.9	MEG_3763	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN	NA
contig00045	32082	34133	MDTO	0/0	100.0	100.0	MEG_3764	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTO	NA
contig00045	30619	32085	MDTP	0/0	100.0	98.1	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig00142	68	989	MPHA	1/1	100.0	99.7	MEG_4030	Drugs:MLS:Macrolide_phosphotransferases:MPHA	NA
contig00002	117826	118302	MPHB	0/0	100.0	98.3	MEG_4033	Drugs:MLS:Macrolide_phosphotransferases:MPHB	NA
contig00020	40795	42543	MSBA	0/0	100.0	100.0	MEG_4061	Drugs:Multi-drug_resistance:Multi-drug_ABC_efflux_pumps:MSBA	NA
contig00037	15236	15568	MVRC	0/0	100.0	100.0	MEG_4103	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MVRC	NA
contig00021	10335	12236	PBP2	0/0	100.0	100.0	MEG_5400	Drugs:betalactams:Penicillin_binding_protein:PBP2	NA
contig00002	170322	171626	PBP4B	0/0	100.0	99.7	MEG_5409	Drugs:betalactams:Penicillin_binding_protein:PBP4B	NA
contig00044	22851	23819	PMRF	0/0	100.0	100.0	MEG_5801	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF	NA
contig00052	21713	22582	ROBA	0/0	100.0	99.0	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00045	8453	8775	SOXS	0/0	99.7	99.7	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00086	6147	6962	SULII	0/0	100.0	100.0	MEG_6617	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULII	NA
contig00086	2989	4234	TEM	0/0	98.3	99.4	MEG_6875	Drugs:betalactams:Class_A_betalactamases:TEM	NA
contig00043	35270	36913	YOGI	0/0	100.0	98.2	MEG_7842	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:YOGI	NA

ID019

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00042	19259	20062	aph(3’’)-Ib_5	0/0	100.0	100.0	AF321551	aph(3’’)-Ib	Streptomycin
contig00042	18423	19259	aph(6)-Id_1	0/0	100.0	100.0	M28829	aph(6)-Id	Streptomycin
contig00042	13145	14020	blaCTX-M-15_1	0/0	100.0	100.0	AY044436	blaCTX-M-15	Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig00042	16842	17702	blaTEM-1B_1	0/0	100.0	100.0	AY458016	blaTEM-1B	Amoxicillin, Ampicillin, Cephalothin, Piperacillin, Ticarcillin
contig00063	181	663	dfrA14_5	0/0	100.0	99.6	DQ388123	dfrA14	Trimethoprim
contig00010	29799	31031	mdf(A)_1	0/0	100.0	99.9	Y08743	mdf(A)
contig00042	7848	8504	qnrS1_1	0/0	100.0	100.0	AB187515	qnrS1	Ciprofloxacin
contig00042	20123	20938	sul2_2	0/0	100.0	100.0	AY034138	sul2	Sulfamethoxazole
contig00033	41311	42557	tet(A)_6	0/0	97.8	100.0	AF534183	tet(A)	Doxycycline, Tetracycline

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00013	38652	41801	acrB	0/0	100.0	99.6	U00096.3:484403-481253	Protein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug/proton antiporter.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00002	162052	165165	acrD	0/0	100.0	99.1	AP009048.1:2586250-2589364	AcrD is an aminoglycoside efflux pump expressed in E. coli. Its expression can be induced by indole and is regulated by baeRS and cpxAR.	aminoglycoside
contig00012	124669	125826	acrE	0/0	100.0	99.7	U00096:3413863-3415021	AcrE is a membrane fusion protein similar to AcrA.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00012	125838	128942	acrF	0/0	100.0	99.6	U00096:3415032-3418137	AcrF is a inner membrane transporter similar to AcrB.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00012	123608	124270	acrS	0/0	100.0	99.1	U00096:3413465-3412802	AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.	cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00042	19259	20062	APH(3’’)-Ib	0/0	100.0	99.8	AF313472:15593-16397	APH(3’’)-Ib is an aminoglycoside phosphotransferase encoded by plasmids transposons integrative conjugative elements and chromosomes in Enterobacteriaceae and Pseudomonas spp.	aminoglycoside
contig00042	18423	19259	APH(6)-Id	0/0	100.0	99.9	AF024602:3155-3992	APH(6)-Id is an aminoglycoside phosphotransferase encoded by plasmids integrative conjugative elements and chromosomal genomic islands in K. pneumoniae Salmonella spp. E. coli Shigella flexneri Providencia alcalifaciens Pseudomonas spp. V. cholerae Edwardsiella tarda Pasteurella multocida and Aeromonas bestiarum	aminoglycoside
contig00049	14111	14932	bacA	0/0	100.0	99.5	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00003	87518	88240	baeR	0/0	100.0	100.0	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00003	86118	87521	baeS	0/0	100.0	100.0	AP009048:2165012-2166416	BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.	aminocoumarin, aminoglycoside
contig00016	22469	23842	cpxA	0/0	100.0	99.0	BA000007.3:4905062-4903688	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	aminocoumarin, aminoglycoside
contig00009	15081	15713	CRP	0/0	100.0	99.4	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00042	13145	14020	CTX-M-15	0/0	100.0	100.0	AY044436:1435-2311	CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family	cephalosporin
contig00063	181	663	dfrA14	0/0	100.0	99.8	EU780012:2162-2645	dfrA14 is an integron-encoded dihydrofolate reductase found in Escherichia coli	diaminopyrimidine
contig00005	19890	21062	emrA	0/0	100.0	99.8	AP009048:2810082-2811255	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	fluoroquinolone
contig00005	21079	22617	emrB	0/0	100.0	100.0	U00096:2812615-2814154	emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin.	fluoroquinolone
contig00002	64872	65927	emrK	0/0	100.0	99.2	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00005	19233	19763	emrR	0/0	100.0	100.0	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00002	63334	64872	emrY	0/0	100.0	98.6	D78168:1591-3130	emrY is a multidrug transport that moves substrates across the inner membrane of the Gram-negative E. coli. It is a homolog of emrB.	tetracycline
contig00008	145790	147433	eptA	0/0	100.0	99.9	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00013	37436	38629	Escherichia_coli_acrA	0/0	100.0	99.8	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00008	102435	103568	Escherichia_coli_ampC	0/0	100.0	98.8	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00002	129149	130453	Escherichia_coli_ampC1_beta-lactamase	0/0	100.0	96.9	FN649414.1:2765050-2766355	An ampC-like beta-lactamase identified from Escherichia coli.	cephalosporin, penam
contig00013	126663	127820	Escherichia_coli_ampH	0/0	100.0	98.9	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig00010	29799	31031	Escherichia_coli_mdfA	0/0	100.0	98.4	JQ394987:0-1233	Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter.	benzalkonium_chloride, rhodamine, tetracycline
contig00002	66451	67065	evgA	0/0	100.0	100.0	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00002	67070	70663	evgS	0/0	100.0	99.1	U00096:2484373-2487967	EvgS is a sensor protein that phosphorylates the regulatory protein EvgA. evgS corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	fluoroquinolone, macrolide, penam, tetracycline
contig00034	1784	2512	gadW	0/0	100.0	94.5	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig00034	592	1416	gadX	0/0	100.0	99.9	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00020	76181	76594	H-NS	0/0	100.0	99.3	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00011	8520	9197	kdpE	0/0	100.0	97.8	U00096.3:721733-721055	kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding.	aminoglycoside
contig00026	47406	47789	marA	0/0	100.0	99.7	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00003	77258	78505	mdtA	0/0	100.0	100.0	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00003	78505	81627	mdtB	0/0	100.0	97.9	U00096:2155262-2158385	MdtB is a transporter that forms a heteromultimer complex with MdtC to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex.	aminocoumarin
contig00003	81628	84705	mdtC	0/0	100.0	98.4	U00096:2158385-2161463	MdtC is a transporter that forms a heteromultimer complex with MdtB to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex. In the absence of MdtB MdtC can form a homomultimer complex that results in a functioning efflux complex with a narrower drug specificity. mdtC corresponds to 3 loci in Pseudomonas aeruginosa PAO1 (gene name: muxC/muxB) and 3 loci in Pseudomonas aeruginosa LESB58.	aminocoumarin
contig00034	6013	7170	mdtE	0/0	100.0	99.7	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00034	2875	5988	mdtF	0/0	100.0	99.9	U00096:3660413-3663527	MdtF is the multidrug inner membrane transporter for the MdtEF-TolC efflux complex.	fluoroquinolone, macrolide, penam
contig00006	16859	18085	mdtG	0/0	100.0	99.4	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00006	26714	27922	mdtH	0/0	100.0	98.3	U00096:1125326-1124117	Multidrug resistance protein MdtH	fluoroquinolone
contig00001	306734	307966	mdtM	0/0	100.0	97.2	U00096.3:4568519-4567286	Multidrug resistance protein MdtM	acridine_dye, fluoroquinolone, lincosamide, nucleoside, phenicol
contig00014	21821	22852	mdtN	0/0	100.0	99.9	AP009048.1:4307588-4306556	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	acridine_dye, nucleoside
contig00014	22852	24903	mdtO	0/0	100.0	100.0	AP009048.1:4306557-4304505	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00014	24900	26366	mdtP	0/0	100.0	99.9	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00002	186442	186916	mphB	0/0	99.6	97.3	AE005174.2:3397370-3397847	The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides.	macrolide
contig00007	51483	53231	msbA	0/0	100.0	100.0	U00096.3:966620-968369	MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability.	nitroimidazole
contig00027	22973	23941	pmrF	0/0	100.0	99.5	U00096:2367070-2368039	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide
contig00042	7848	8504	QnrS1	0/0	100.0	100.0	DQ485529.1:0-657	QnrS1 is a plasmid-mediated quinolone resistance protein found in Shigella flexneri	fluoroquinolone
contig00042	20123	20938	sul2	0/0	100.0	100.0	AY055428.1:21084-20268	Sul2 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria usually found on small plasmids.	sulfonamide
contig00042	16842	17702	TEM-1	0/0	100.0	99.9	AL513383:161910-162771	TEM-1 is a broad-spectrum beta-lactamase found in many Gram-negative bacteria. Confers resistance to penicillins and first generation cephalosphorins.	cephalosporin, monobactam, penam, penem
contig00033	41311	42557	tet(A)	0/0	97.8	100.0	AF534183.1:2970-4245	TetA is a tetracycline efflux pump found in many species of Gram-negative bacteria.	tetracycline
contig00028	41766	43253	tolC	0/0	100.0	99.7	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan
contig00003	16782	17948	ugd	0/0	100.0	96.9	U00096:2099613-2098446	PmrE is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin	peptide
contig00003	254445	256088	yojI	0/0	100.0	98.2	U00096.3:2308615-2306971	YojI mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. YojI is capable of pumping out microcin molecules. The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI.	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00042	19259	20062	(AGly)strA	0/0	100	99.9	AB366441:22458-23261	(AGly)strA	NA
contig00042	18423	19259	(AGly)strB	0/0	100	100.0	FJ474091:264-1100	(AGly)strB	NA
contig00002	129149	130453	(Bla)AmpC1_Ecoli	0/0	100	96.9	FN649414:2765051-2766355	(Bla)AmpC1_Ecoli	NA
contig00008	102435	103568	(Bla)AmpC2_Ecoli	0/0	100	98.8	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00013	126663	127820	(Bla)ampH_Ecoli	0/0	100	98.9	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00042	13145	14020	(Bla)blaCTX-M-15	0/0	100	100.0	JQ686199:261-1136	(Bla)blaCTX-M-15	NA
contig00042	16842	17702	(Bla)blaTEM-105	0/0	100	99.9	AF516720:215-1075	(Bla)blaTEM-105	NA
contig00011	62026	63927	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100	99.7	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA
contig00042	7848	8504	(Flq)qnr-S1	0/0	100	100.0	AB187515:9737-10393	(Flq)qnr-S1	NA
contig00042	20123	20938	(Sul)sul2	0/0	100	100.0	EU360945:1617-2432	(Sul)sul2	NA
contig00033	41283	42557	(Tet)tetA	0/0	100	100.0	JX424423:94438-95712	(Tet)tetA	NA
contig00063	181	654	(Tmt)dfrA14	0/0	100	100.0	GU726917:72-545	(Tmt)dfrA14	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00042	19259	20086	aph(3’’)-Ib	0/0	100	100.0	NG_056002.2	aminoglycoside O-phosphotransferase APH(3’’)-Ib	STREPTOMYCIN
contig00042	18423	19259	aph(6)-Id	0/0	100	100.0	NG_047464.1	aminoglycoside O-phosphotransferase APH(6)-Id	STREPTOMYCIN
contig00042	13145	14020	blaCTX-M-15	0/0	100	100.0	NG_048935.1	class A extended-spectrum beta-lactamase CTX-M-15	CEPHALOSPORIN
contig00008	102435	103568	blaEC	0/0	100	99.7	NG_047496.1	BlaEC family class C beta-lactamase	BETA-LACTAM
contig00042	16842	17702	blaTEM-1	0/0	100	100.0	NG_050145.1	class A broad-spectrum beta-lactamase TEM-1	BETA-LACTAM
contig00063	181	654	dfrA14	0/0	100	100.0	NG_056035.1	trimethoprim-resistant dihydrofolate reductase DfrA14	TRIMETHOPRIM
contig00042	7848	8504	qnrS1	0/0	100	100.0	NG_050543.1	quinolone resistance pentapeptide repeat protein QnrS1	QUINOLONE
contig00042	20123	20938	sul2	0/0	100	100.0	NG_051852.1	sulfonamide-resistant dihydropteroate synthase Sul2	SULFONAMIDE
contig00033	41283	42482	tet(A)	0/0	100	100.0	NG_048154.1	tetracycline efflux MFS transporter Tet(A)	TETRACYCLINE

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00013	37436	38629	ACRA	0/0	100.0	99.8	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00013	38652	41801	ACRB	0/0	100.0	99.6	MEG_401	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRB	NA
contig00002	162052	165165	ACRD	0/0	100.0	99.1	MEG_407	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ACRD	NA
contig00012	124669	125826	ACRE	0/0	100.0	99.7	MEG_408	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRE	NA
contig00012	125838	128942	ACRF	0/0	100.0	99.6	MEG_409	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRF	NA
contig00012	123608	124270	ACRS	0/0	100.0	99.1	MEG_415	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS	NA
contig00013	126663	127820	AMPH	0/0	100.0	98.9	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00042	19259	20086	APH3-DPRIME	0/0	100.0	100.0	MEG_1019	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH3-DPRIME	NA
contig00042	18423	19259	APH6	0/0	100.0	100.0	MEG_1086	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH6	NA
contig00003	63003	64855	ASMA	0/0	100.0	98.1	MEG_1180	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:ASMA	NA
contig00049	14111	14932	BACA	0/0	100.0	99.5	MEG_1189	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00003	87518	88240	BAER	0/0	100.0	100.0	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00003	86118	87521	BAES	0/0	100.0	100.0	MEG_1193	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES	NA
contig00003	204672	205862	BCR	0/0	100.0	100.0	MEG_1210	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR	NA
contig00008	102435	103568	BLAEC	0/0	100.0	99.7	MEG_1276	Drugs:betalactams:Class_C_betalactamases:BLAEC	NA
contig00016	21774	22472	CPXAR	0/0	100.0	99.9	MEG_2122	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00016	22469	23842	CPXAR	0/0	100.0	99.8	MEG_2121	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00009	15081	15713	CRP	0/0	100.0	99.4	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00063	181	654	DFRA	0/0	100.0	99.8	MEG_2517	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00005	19890	21062	EMRA	0/0	100.0	99.8	MEG_2722	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA	NA
contig00005	21079	22617	EMRB	0/0	100.0	100.0	MEG_2725	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRB	NA
contig00033	16352	17542	EMRD	0/0	100.0	100.0	MEG_2729	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD	NA
contig00002	64872	66035	EMRK	0/0	100.0	99.2	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig00005	19233	19763	EMRR	0/0	100.0	100.0	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00002	63334	64872	EMRY	0/0	100.0	98.6	MEG_2736	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRY	NA
contig00008	145790	147433	EPTA	0/0	100.0	99.9	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig00002	67070	70663	EVGS	0/0	100.0	99.1	MEG_2870	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EVGS	NA
contig00034	1784	2512	GADW	0/0	100.0	99.9	MEG_3081	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig00034	592	1416	GADX	0/0	100.0	99.9	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00020	76181	76594	HNS	0/0	100.0	99.3	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00011	8520	9197	KDPE	0/0	100.0	97.8	MEG_3448	Drugs:Aminoglycosides:Aminoglycoside_efflux_pumps:KDPE	NA
contig00026	47400	47789	MARA	0/0	100.0	99.7	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00026	46951	47385	MARR	0/0	100.0	98.4	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00010	29799	31031	MDFA	0/0	100.0	100.0	MEG_3737	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDFA	NA
contig00003	77258	78505	MDTA	0/0	100.0	100.0	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00003	78505	81627	MDTB	0/0	100.0	97.9	MEG_3747	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTB	NA
contig00003	81628	84705	MDTC	0/0	100.0	98.4	MEG_3749	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTC	NA
contig00034	6013	7170	MDTE	0/0	100.0	99.7	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00034	2875	5988	MDTF	0/0	100.0	99.9	MEG_3752	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTF	NA
contig00006	16859	18085	MDTG	0/0	100.0	100.0	MEG_3753	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig00006	26714	27922	MDTH	0/0	100.0	98.3	MEG_3755	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTH	NA
contig00031	21649	21978	MDTI	0/0	100.0	99.7	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00031	21965	22330	MDTJ	0/0	100.0	99.5	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00004	164081	165454	MDTK	0/0	100.0	98.8	MEG_3759	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:MDTK	NA
contig00001	306734	307966	MDTM	0/0	100.0	97.2	MEG_3761	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTM	NA
contig00014	21821	22852	MDTN	0/0	100.0	99.9	MEG_3763	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN	NA
contig00014	22852	24903	MDTO	0/0	100.0	100.0	MEG_3764	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTO	NA
contig00014	24900	26366	MDTP	0/0	100.0	99.9	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig00002	186442	186916	MPHB	0/0	99.6	97.3	MEG_4033	Drugs:MLS:Macrolide_phosphotransferases:MPHB	NA
contig00007	51483	53231	MSBA	0/0	100.0	100.0	MEG_4061	Drugs:Multi-drug_resistance:Multi-drug_ABC_efflux_pumps:MSBA	NA
contig00011	62026	63927	PBP2	0/0	100.0	99.7	MEG_5400	Drugs:betalactams:Penicillin_binding_protein:PBP2	NA
contig00002	129149	130453	PBP4B	0/0	100.0	96.9	MEG_5409	Drugs:betalactams:Penicillin_binding_protein:PBP4B	NA
contig00027	22973	23941	PMRF	0/0	100.0	99.5	MEG_5801	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF	NA
contig00042	7848	8504	QNRS	0/0	100.0	100.0	MEG_6020	Drugs:Fluoroquinolones:Quinolone_resistance_protein_Qnr:QNRS	NA
contig00001	229542	230411	ROBA	0/0	100.0	99.1	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00014	48323	48645	SOXS	0/0	99.7	99.7	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00042	20123	20938	SULII	0/0	100.0	100.0	MEG_6617	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULII	NA
contig00042	16475	17720	TEM	0/0	98.3	99.4	MEG_6875	Drugs:betalactams:Class_A_betalactamases:TEM	NA
contig00033	41283	42557	TETA	0/0	100.0	100.0	MEG_7024	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETA	NA
contig00003	16782	17948	UGD	0/0	100.0	96.9	MEG_7328	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:UGD	NA
contig00003	254445	256088	YOGI	0/0	100.0	98.2	MEG_7842	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:YOGI	NA

ID01CT

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00093	1696	2556	aac(3)-IIa_1	0/0	100.0	99.8	X51534	aac(3)-IIa	Gentamicin, Tobramycin
contig00097	1539	2138	aac(6’)-Ib-cr_1	0/0	100.0	100.0	DQ303918	aac(6’)-Ib-cr	Ciprofloxacin
contig00092	925	1889	ant(3’’)-Ia_1	3/7	99.3	99.1	X02340	ant(3’’)-Ia	Streptomycin
contig00095	831	1634	aph(3’’)-Ib_5	0/0	100.0	100.0	AF321551	aph(3’’)-Ib	Streptomycin
contig00095	1	831	aph(6)-Id_1	0/0	99.3	100.0	M28829	aph(6)-Id	Streptomycin
contig00089	2484	3026	ARR-3_4	0/0	100.0	99.5	FM207631	ARR-3
contig00078	2385	3260	blaCTX-M-15_1	0/0	100.0	100.0	AY044436	blaCTX-M-15	Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig00097	578	1408	blaOXA-1_1	0/0	100.0	100.0	HQ170510	blaOXA-1	Amoxicillin, Amoxicillin+Clavulanic_acid, Ampicillin, Ampicillin+Clavulanic_acid, Cefepime, Piperacillin, Piperacillin+Tazobactam
contig00089	1083	1883	blaOXA-10_1	0/0	100.0	100.0	J03427	blaOXA-10	Amoxicillin, Ampicillin, Aztreonam, Piperacillin, Piperacillin+Tazobactam
contig00100	706	1566	blaTEM-1B_1	0/0	100.0	100.0	AY458016	blaTEM-1B	Amoxicillin, Ampicillin, Cephalothin, Piperacillin, Ticarcillin
contig00079	350	1009	catA1_1	0/0	100.0	99.8	V00622	catA1	Chloramphenicol
contig00115	128	701	dfrA7_5	3/4	100.0	98.8	AJ419170	dfrA7	Trimethoprim
contig00005	49333	50565	mdf(A)_1	0/0	100.0	99.9	Y08743	mdf(A)
contig00110	69	990	mph(A)_2	1/1	100.0	99.7	U36578	mph(A)	Erythromycin, Azithromycin, Spiramycin, Telithromycin
contig00080	4404	5048	qnrB1_1	0/0	100.0	100.0	DQ351241	qnrB1	Ciprofloxacin
contig00091	691	1937	tet(A)_6	0/0	97.8	100.0	AF534183	tet(A)	Doxycycline, Tetracycline

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00093	1696	2556	AAC(3)-IIe	0/0	100.0	99.5	EU022315.1:0-861	AAC(3)-IIe is a plasmid-encoded aminoglycoside acetyltransferase in E. coli	aminoglycoside
contig00097	1539	2138	AAC(6’)-Ib-cr	0/0	100.0	100.0	DQ303918:0-600	AAC(6’)-Ib-cr is an aminoglycoside acetyltransferase encoded by plasmids transposons integrons in Enterobacteriaceae. The aac(6’)-Ib-cr variant gene can induce resistance against aminoglycoside and fluoroquinolone simultaneously	aminoglycoside, fluoroquinolone
contig00001	89130	92279	acrB	0/0	100.0	100.0	U00096.3:484403-481253	Protein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug/proton antiporter.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00007	71357	74470	acrD	0/0	100.0	100.0	AP009048.1:2586250-2589364	AcrD is an aminoglycoside efflux pump expressed in E. coli. Its expression can be induced by indole and is regulated by baeRS and cpxAR.	aminoglycoside
contig00031	8641	9798	acrE	0/0	100.0	99.9	U00096:3413863-3415021	AcrE is a membrane fusion protein similar to AcrA.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00031	5525	8629	acrF	0/0	100.0	99.5	U00096:3415032-3418137	AcrF is a inner membrane transporter similar to AcrB.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00031	10197	10859	acrS	0/0	100.0	100.0	U00096:3413465-3412802	AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.	cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00092	925	1889	ANT(3’’)-IIa	3/7	99.3	99.1	X02340.1:222-1194	ANT(3’’)-IIa is a aminoglycoside nucleotidyltransferase identified in Acinetobacter spp. via horizontal gene transfer mechanisms.	aminoglycoside
contig00095	831	1634	APH(3’’)-Ib	0/0	100.0	99.8	AF313472:15593-16397	APH(3’’)-Ib is an aminoglycoside phosphotransferase encoded by plasmids transposons integrative conjugative elements and chromosomes in Enterobacteriaceae and Pseudomonas spp.	aminoglycoside
contig00095	1	831	APH(6)-Id	0/0	99.3	99.9	AF024602:3155-3992	APH(6)-Id is an aminoglycoside phosphotransferase encoded by plasmids integrative conjugative elements and chromosomal genomic islands in K. pneumoniae Salmonella spp. E. coli Shigella flexneri Providencia alcalifaciens Pseudomonas spp. V. cholerae Edwardsiella tarda Pasteurella multocida and Aeromonas bestiarum	aminoglycoside
contig00089	2484	2936	arr-3	0/0	100.0	100.0	EU675686:1956-2409	arr-3 is a plasmid-encoded ribosyltransferase found in Vibrio fluvialis	rifamycin
contig00004	30105	30926	bacA	0/0	100.0	100.0	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00016	102927	103649	baeR	0/0	100.0	100.0	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00016	101527	102930	baeS	0/0	100.0	99.9	AP009048:2165012-2166416	BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.	aminocoumarin, aminoglycoside
contig00079	350	1009	catI	0/0	100.0	99.8	V00622:243-903	catI is a chromosome and transposon-encoded variant of the cat gene found in Escherichia coli and Acinetobacter baumannii	phenicol
contig00018	61611	62984	cpxA	0/0	100.0	99.0	BA000007.3:4905062-4903688	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	aminocoumarin, aminoglycoside
contig00006	15313	15945	CRP	0/0	100.0	99.4	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00078	2385	3260	CTX-M-15	0/0	100.0	100.0	AY044436:1435-2311	CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family	cephalosporin
contig00115	228	701	dfrA7	0/0	100.0	100.0	FJ854362:2338-2812	dfrA7 is an integron-encoded dihydrofolate reductase found in Escherichia coli	diaminopyrimidine
contig00015	29893	31065	emrA	0/0	100.0	99.9	AP009048:2810082-2811255	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	fluoroquinolone
contig00015	31082	32620	emrB	0/0	100.0	99.9	U00096:2812615-2814154	emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin.	fluoroquinolone
contig00048	2768	3823	emrK	0/0	100.0	99.8	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00015	29236	29766	emrR	0/0	100.0	100.0	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00048	1230	2768	emrY	0/0	100.0	99.0	D78168:1591-3130	emrY is a multidrug transport that moves substrates across the inner membrane of the Gram-negative E. coli. It is a homolog of emrB.	tetracycline
contig00036	7751	9394	eptA	0/0	100.0	100.0	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00001	87914	89107	Escherichia_coli_acrA	0/0	100.0	100.0	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00010	120713	121847	Escherichia_coli_ampC	1/1	100.0	97.3	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00007	105869	107173	Escherichia_coli_ampC1_beta-lactamase	0/0	100.0	100.0	FN649414.1:2765050-2766355	An ampC-like beta-lactamase identified from Escherichia coli.	cephalosporin, penam
contig00001	177246	178403	Escherichia_coli_ampH	0/0	100.0	98.9	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig00005	49333	50565	Escherichia_coli_mdfA	0/0	100.0	98.4	JQ394987:0-1233	Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter.	benzalkonium_chloride, rhodamine, tetracycline
contig00048	4347	4961	evgA	0/0	100.0	100.0	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00048	4966	8559	evgS	0/0	100.0	99.7	U00096:2484373-2487967	EvgS is a sensor protein that phosphorylates the regulatory protein EvgA. evgS corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	fluoroquinolone, macrolide, penam, tetracycline
contig00024	32273	33001	gadW	0/0	100.0	94.7	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig00024	31081	31905	gadX	0/0	100.0	100.0	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00002	147432	147845	H-NS	0/0	100.0	99.5	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00003	93542	94219	kdpE	0/0	100.0	100.0	U00096.3:721733-721055	kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding.	aminoglycoside
contig00022	63335	63718	marA	0/0	100.0	99.7	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00016	92673	93914	mdtA	1/6	99.5	96.9	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00016	93914	97036	mdtB	0/0	100.0	97.0	U00096:2155262-2158385	MdtB is a transporter that forms a heteromultimer complex with MdtC to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex.	aminocoumarin
contig00016	97037	100114	mdtC	0/0	100.0	97.0	U00096:2158385-2161463	MdtC is a transporter that forms a heteromultimer complex with MdtB to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex. In the absence of MdtB MdtC can form a homomultimer complex that results in a functioning efflux complex with a narrower drug specificity. mdtC corresponds to 3 loci in Pseudomonas aeruginosa PAO1 (gene name: muxC/muxB) and 3 loci in Pseudomonas aeruginosa LESB58.	aminocoumarin
contig00024	36502	37659	mdtE	0/0	100.0	100.0	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00024	33364	36477	mdtF	0/0	100.0	99.9	U00096:3660413-3663527	MdtF is the multidrug inner membrane transporter for the MdtEF-TolC efflux complex.	fluoroquinolone, macrolide, penam
contig00012	21234	22460	mdtG	0/0	100.0	99.3	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00012	31089	32297	mdtH	0/0	100.0	99.9	U00096:1125326-1124117	Multidrug resistance protein MdtH	fluoroquinolone
contig00061	9725	10936	mdtM	0/0	98.3	95.5	U00096.3:4568519-4567286	Multidrug resistance protein MdtM	acridine_dye, fluoroquinolone, lincosamide, nucleoside, phenicol
contig00043	26699	27730	mdtN	0/0	100.0	100.0	AP009048.1:4307588-4306556	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	acridine_dye, nucleoside
contig00043	24648	26699	mdtO	0/0	100.0	99.9	AP009048.1:4306557-4304505	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00043	23185	24651	mdtP	0/0	100.0	100.0	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00110	69	974	mphA	0/0	100.0	100.0	D16251.1:2531-1625	The mphA gene encodes for resistance enzyme MPH(2’)-I which preferentially inactivate 14-membered macrolides (e.g.erythromycin telithromycin roxithromycin) over 16-membered macrolides (e.g.tylosin spiramycin). It phosphorylates macrolides at 2’-OH hydroxyl of desosamine sugar of macrolides in a GTP-dependent manner.	macrolide
contig00007	50364	50838	mphB	0/0	99.6	97.3	AE005174.2:3397370-3397847	The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides.	macrolide
contig00011	40850	42598	msbA	0/0	100.0	100.0	U00096.3:966620-968369	MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability.	nitroimidazole
contig00097	578	1408	OXA-1	0/0	100.0	100.0	JN420336.1:2230-1399	OXA-1 is a beta-lactamase found in E. coli	cephalosporin, penam
contig00089	1083	1883	OXA-10	0/0	100.0	100.0	AF205943:7511-8312	OXA-10 is a beta-lactamase found in Acinetobacter baumannii and P. aeruginosa.	cephalosporin, penam
contig00064	2223	3191	pmrF	0/0	100.0	100.0	U00096:2367070-2368039	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide
contig00080	4367	5048	QnrB17	1/1	100.0	99.1	AM919398:0-681	QnrB17 is a plasmid-mediated quinolone resistance protein found in Citrobacter freundii	fluoroquinolone
contig00100	706	1566	TEM-1	0/0	100.0	99.9	AL513383:161910-162771	TEM-1 is a broad-spectrum beta-lactamase found in many Gram-negative bacteria. Confers resistance to penicillins and first generation cephalosphorins.	cephalosporin, monobactam, penam, penem
contig00091	691	1937	tet(A)	0/0	97.8	100.0	AF534183.1:2970-4245	TetA is a tetracycline efflux pump found in many species of Gram-negative bacteria.	tetracycline
contig00004	6260	7747	tolC	0/0	100.0	99.7	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan
contig00016	38819	39985	ugd	0/0	100.0	98.8	U00096:2099613-2098446	PmrE is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin	peptide
contig00029	56236	57879	yojI	0/0	100.0	100.0	U00096.3:2308615-2306971	YojI mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. YojI is capable of pumping out microcin molecules. The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI.	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00093	1696	2556	(AGly)aac3-IIa	0/0	100.0	99.8	X51534:91-951	(AGly)aac3-IIa	NA
contig00092	925	1736	(AGly)aadA1-pm	0/0	97.7	99.9	JQ690540:7968-8798	(AGly)aadA1-pm	NA
contig00095	831	1634	(AGly)strA	0/0	100.0	99.9	AB366441:22458-23261	(AGly)strA	NA
contig00095	1	831	(AGly)strB	0/0	99.3	100.0	FJ474091:264-1100	(AGly)strB	NA
contig00007	105869	107173	(Bla)AmpC1_Ecoli	0/0	100.0	100.0	FN649414:2765051-2766355	(Bla)AmpC1_Ecoli	NA
contig00010	120713	121847	(Bla)AmpC2_Ecoli	1/1	100.0	97.3	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00001	177246	178403	(Bla)ampH_Ecoli	0/0	100.0	98.9	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00078	2385	3260	(Bla)blaCTX-M-15	0/0	100.0	100.0	JQ686199:261-1136	(Bla)blaCTX-M-15	NA
contig00097	578	1408	(Bla)blaOXA-1	0/0	100.0	100.0	JQ682867:1-831	(Bla)blaOXA-1	NA
contig00089	1083	1883	(Bla)blaOXA-10	0/0	100.0	100.0	HQ386834:1465-2265	(Bla)blaOXA-10	NA
contig00100	706	1566	(Bla)blaTEM-105	0/0	100.0	99.9	AF516720:215-1075	(Bla)blaTEM-105	NA
contig00003	145923	147824	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100.0	100.0	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA
contig00080	4367	5048	(Flq)qnrB1	1/1	100.0	99.8	DQ351241:1-681	(Flq)qnrB1	NA
contig00110	69	974	(MLS)mph(A)	0/0	100.0	100.0	DQ445270:1626-2531	(MLS)mph(A)	NA
contig00079	350	1009	(Phe)catA1	0/0	100.0	99.8	V00622:244-903	(Phe)catA1	NA
contig00089	2484	2936	(Rif)arr3	0/0	100.0	100.0	JF806499:1353-1805	(Rif)arr3	NA
contig00091	691	1965	(Tet)tetA	0/0	100.0	100.0	JX424423:94438-95712	(Tet)tetA	NA
contig00091	10	660	(Tet)tetR	0/0	100.0	100.0	HF545434:53576-54226	(Tet)tetR	NA
contig00115	228	701	(Tmt)dhfr7	0/0	100.0	100.0	X58425:594-1067	(Tmt)dhfr7	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00093	1696	2556	aac(3)-IIe	0/0	100.0	99.8	NG_047244.1	aminoglycoside N-acetyltransferase AAC(3)-IIe	GENTAMICIN
contig00097	1539	2093	aac(6’)-Ib-D181Y	0/0	100.0	99.8	NG_067946.1	AAC(6’)-Ib family aminoglycoside 6’-N-acetyltransferase	AMIKACIN, KANAMYCIN, TOBRAMYCIN
contig00089	1913	2353	aacA34	0/0	100.0	100.0	NG_047319.1	aminoglycoside 6’-N-acetyltransferase AacA34	AMINOGLYCOSIDE
contig00092	925	1716	aadA1	0/0	100.0	100.0	NG_052536.1	ANT(3’’)-Ia family aminoglycoside nucleotidyltransferase AadA1	STREPTOMYCIN
contig00095	831	1658	aph(3’’)-Ib	0/0	100.0	100.0	NG_056002.2	aminoglycoside O-phosphotransferase APH(3’’)-Ib	STREPTOMYCIN
contig00095	1	831	aph(6)-Id	0/0	99.3	100.0	NG_047464.1	aminoglycoside O-phosphotransferase APH(6)-Id	STREPTOMYCIN
contig00089	2484	2936	arr-3	0/0	100.0	100.0	NG_048581.1	NAD(+)–rifampin ADP-ribosyltransferase Arr-3	RIFAMYCIN
contig00078	2385	3260	blaCTX-M-15	0/0	100.0	100.0	NG_048935.1	class A extended-spectrum beta-lactamase CTX-M-15	CEPHALOSPORIN
contig00010	120713	121847	blaEC-15	1/1	100.0	98.5	NG_049081.1	class C extended-spectrum beta-lactamase EC-15	CEPHALOSPORIN
contig00097	578	1408	blaOXA-1	0/0	100.0	100.0	NG_049392.1	oxacillin-hydrolyzing class D beta-lactamase OXA-1	CEPHALOSPORIN
contig00089	1083	1883	blaOXA-10	0/0	100.0	100.0	NG_049393.1	oxacillin-hydrolyzing class D beta-lactamase OXA-10	CEPHALOSPORIN
contig00100	706	1566	blaTEM-1	0/0	100.0	100.0	NG_050145.1	class A broad-spectrum beta-lactamase TEM-1	BETA-LACTAM
contig00079	350	1009	catA1	0/0	100.0	99.8	NG_047582.1	type A-1 chloramphenicol O-acetyltransferase	CHLORAMPHENICOL
contig00115	228	701	dfrA7	0/0	100.0	100.0	NG_047737.1	trimethoprim-resistant dihydrofolate reductase DfrA7	TRIMETHOPRIM
contig00110	69	990	mph(A)	1/1	100.0	99.7	NG_047986.1	Mph(A) family macrolide 2’-phosphotransferase	MACROLIDE
contig00080	4404	5048	qnrB1	0/0	100.0	100.0	NG_050469.1	quinolone resistance pentapeptide repeat protein QnrB1	QUINOLONE
contig00091	766	1965	tet(A)	0/0	100.0	100.0	NG_048154.1	tetracycline efflux MFS transporter Tet(A)	TETRACYCLINE

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00093	1696	2556	AAC3	0/0	100.0	99.8	MEG_44	Drugs:Aminoglycosides:Aminoglycoside_N-acetyltransferases:AAC3	NA
contig00001	87914	89107	ACRA	0/0	100.0	100.0	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00001	89130	92279	ACRB	0/0	100.0	100.0	MEG_401	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRB	NA
contig00007	71357	74470	ACRD	0/0	100.0	100.0	MEG_407	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ACRD	NA
contig00031	8641	9798	ACRE	0/0	100.0	99.9	MEG_408	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRE	NA
contig00031	5525	8629	ACRF	0/0	100.0	99.5	MEG_409	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRF	NA
contig00031	10197	10859	ACRS	0/0	100.0	100.0	MEG_415	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS	NA
contig00001	177246	178403	AMPH	0/0	100.0	98.9	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00092	925	1889	ANT3-DPRIME	3/7	99.3	99.1	MEG_949	Drugs:Aminoglycosides:Aminoglycoside_O-nucleotidyltransferases:ANT3-DPRIME	NA
contig00095	831	1658	APH3-DPRIME	0/0	100.0	100.0	MEG_1019	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH3-DPRIME	NA
contig00095	1	831	APH6	0/0	99.3	100.0	MEG_1086	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH6	NA
contig00089	2484	3026	ARR	0/0	100.0	99.5	MEG_1135	Drugs:Rifampin:Rifampin_ADP-ribosyltransferase_Arr:ARR	NA
contig00016	79213	81065	ASMA	0/0	100.0	97.6	MEG_1180	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:ASMA	NA
contig00004	30105	30926	BACA	0/0	100.0	100.0	MEG_1190	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00016	102927	103649	BAER	0/0	100.0	100.0	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00016	101527	102930	BAES	0/0	100.0	99.9	MEG_1193	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES	NA
contig00041	19031	20221	BCR	0/0	100.0	100.0	MEG_1210	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR	NA
contig00010	120713	121847	BLAEC	1/1	100.0	98.5	MEG_1282	Drugs:betalactams:Class_C_betalactamases:BLAEC	NA
contig00079	339	1009	CATA	0/0	100.0	100.0	MEG_1593	Drugs:Phenicol:Chloramphenicol_acetyltransferases:CATA	NA
contig00018	60916	61614	CPXAR	0/0	100.0	100.0	MEG_2122	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00018	61611	62984	CPXAR	0/0	100.0	100.0	MEG_2121	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00006	15313	15945	CRP	0/0	100.0	99.4	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00115	228	701	DFRA	0/0	100.0	100.0	MEG_2548	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00015	29893	31065	EMRA	0/0	100.0	99.9	MEG_2722	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA	NA
contig00015	31082	32620	EMRB	0/0	100.0	99.9	MEG_2725	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRB	NA
contig00045	35047	36237	EMRD	0/0	100.0	100.0	MEG_2729	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD	NA
contig00048	2768	3931	EMRK	0/0	100.0	99.8	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig00015	29236	29766	EMRR	0/0	100.0	100.0	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00048	1230	2768	EMRY	0/0	100.0	99.1	MEG_2736	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRY	NA
contig00036	7751	9394	EPTA	0/0	100.0	100.0	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig00048	4966	8559	EVGS	0/0	100.0	99.7	MEG_2870	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EVGS	NA
contig00024	32273	33001	GADW	0/0	100.0	100.0	MEG_3081	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig00024	31081	31905	GADX	0/0	100.0	100.0	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00002	147432	147845	HNS	0/0	100.0	99.5	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00003	93542	94219	KDPE	0/0	100.0	100.0	MEG_3448	Drugs:Aminoglycosides:Aminoglycoside_efflux_pumps:KDPE	NA
contig00022	63329	63718	MARA	0/0	100.0	99.7	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00022	62880	63314	MARR	0/0	100.0	98.4	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00005	49333	50565	MDFA	0/0	100.0	100.0	MEG_3737	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDFA	NA
contig00016	92673	93914	MDTA	1/6	99.5	96.9	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00016	93914	97036	MDTB	0/0	100.0	97.0	MEG_3747	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTB	NA
contig00016	97037	100114	MDTC	0/0	100.0	97.0	MEG_3749	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTC	NA
contig00024	36502	37659	MDTE	0/0	100.0	100.0	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00024	33364	36477	MDTF	0/0	100.0	99.9	MEG_3752	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTF	NA
contig00012	21234	22460	MDTG	0/0	100.0	99.9	MEG_3753	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig00012	31089	32297	MDTH	0/0	100.0	99.9	MEG_3755	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTH	NA
contig00014	97462	97791	MDTI	0/0	100.0	100.0	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00014	97110	97475	MDTJ	0/0	100.0	99.5	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00014	25708	27081	MDTK	0/0	100.0	100.0	MEG_3759	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:MDTK	NA
contig00061	9725	10936	MDTM	0/0	98.3	95.5	MEG_3761	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTM	NA
contig00043	26699	27730	MDTN	0/0	100.0	100.0	MEG_3763	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN	NA
contig00043	24648	26699	MDTO	0/0	100.0	99.9	MEG_3764	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTO	NA
contig00043	23185	24651	MDTP	0/0	100.0	100.0	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig00110	69	990	MPHA	1/1	100.0	99.7	MEG_4030	Drugs:MLS:Macrolide_phosphotransferases:MPHA	NA
contig00007	50364	50838	MPHB	0/0	99.6	97.3	MEG_4033	Drugs:MLS:Macrolide_phosphotransferases:MPHB	NA
contig00011	40850	42598	MSBA	0/0	100.0	100.0	MEG_4061	Drugs:Multi-drug_resistance:Multi-drug_ABC_efflux_pumps:MSBA	NA
contig00097	578	1408	OXA	0/0	100.0	100.0	MEG_4980	Drugs:betalactams:Class_D_betalactamases:OXA	NA
contig00003	145923	147824	PBP2	0/0	100.0	100.0	MEG_5400	Drugs:betalactams:Penicillin_binding_protein:PBP2	NA
contig00007	105869	107173	PBP4B	0/0	100.0	100.0	MEG_5409	Drugs:betalactams:Penicillin_binding_protein:PBP4B	NA
contig00064	2223	3191	PMRF	0/0	100.0	100.0	MEG_5801	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF	NA
contig00089	734	1081	QACEDELTA1	0/0	100.0	100.0	MEG_5829	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:QACEDELTA1	NA
contig00080	4367	5048	QNRB	1/1	100.0	99.1	MEG_5928	Drugs:Fluoroquinolones:Quinolone_resistance_protein_Qnr:QNRB	NA
contig00028	21739	22608	ROBA	0/0	100.0	98.8	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00043	908	1230	SOXS	0/0	99.7	99.7	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00100	688	1933	TEM	0/0	98.3	99.4	MEG_6875	Drugs:betalactams:Class_A_betalactamases:TEM	NA
contig00091	691	1965	TETA	0/0	100.0	100.0	MEG_7024	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETA	NA
contig00016	38819	39985	UGD	0/0	100.0	98.8	MEG_7328	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:UGD	NA
contig00029	56236	57879	YOGI	0/0	100.0	100.0	MEG_7842	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:YOGI	NA

ID021

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00046	24279	25139	aac(3)-IId_1	0/0	100.0	99.9	EU022314	aac(3)-IId	Gentamicin, Tobramycin
contig00063	901	1702	aadA2_1	0/0	97.9	99.9	NC_010870	aadA2	Streptomycin
contig00010	63505	64380	blaCTX-M-15_1	0/0	100.0	100.0	AY044436	blaCTX-M-15	Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig00046	18447	19307	blaTEM-1B_1	0/0	100.0	100.0	AY458016	blaTEM-1B	Amoxicillin, Ampicillin, Cephalothin, Piperacillin, Ticarcillin
contig00060	5984	6643	catA1_1	0/0	100.0	99.8	V00622	catA1	Chloramphenicol
contig00063	6	503	dfrA12_8	0/0	100.0	100.0	AM040708	dfrA12	Trimethoprim
contig00004	10013	11245	mdf(A)_1	0/0	100.0	99.9	Y08743	mdf(A)
contig00082	68	989	mph(A)_2	1/1	100.0	99.7	U36578	mph(A)	Erythromycin, Azithromycin, Spiramycin, Telithromycin
contig00063	2180	3046	sul1_5	0/0	100.0	99.9	EU780013	sul1	Sulfamethoxazole
contig00067	800	2005	tet(B)_2	0/0	100.0	100.0	AF326777	tet(B)	Doxycycline, Tetracycline, Minocycline

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00046	24279	25139	AAC(3)-IId	0/0	100.0	99.9	EU022314.1:0-861	AAC(3)-IId is a plasmid-encoded aminoglycoside acetyltransferase in E. coli	aminoglycoside
contig00063	923	1702	aadA2	0/0	100.0	99.9	AF156486:5012-5792	aadA2 is an aminoglycoside nucleotidyltransferase gene encoded by plasmids and integrons in K. pneumoniae Salmonella spp. Corynebacterium glutamicum C. freundii and Aeromonas spp.	aminoglycoside
contig00008	39033	42182	acrB	0/0	100.0	100.0	U00096.3:484403-481253	Protein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug/proton antiporter.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00009	71642	74755	acrD	0/0	100.0	100.0	AP009048.1:2586250-2589364	AcrD is an aminoglycoside efflux pump expressed in E. coli. Its expression can be induced by indole and is regulated by baeRS and cpxAR.	aminoglycoside
contig00040	8641	9798	acrE	0/0	100.0	99.9	U00096:3413863-3415021	AcrE is a membrane fusion protein similar to AcrA.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00040	5525	8629	acrF	0/0	100.0	99.9	U00096:3415032-3418137	AcrF is a inner membrane transporter similar to AcrB.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00040	10197	10859	acrS	0/0	100.0	100.0	U00096:3413465-3412802	AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.	cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00003	220493	221314	bacA	0/0	100.0	98.7	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00033	31061	31783	baeR	0/0	100.0	99.5	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00033	31780	33183	baeS	0/0	100.0	99.9	AP009048:2165012-2166416	BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.	aminocoumarin, aminoglycoside
contig00060	5984	6643	catI	0/0	100.0	99.8	V00622:243-903	catI is a chromosome and transposon-encoded variant of the cat gene found in Escherichia coli and Acinetobacter baumannii	phenicol
contig00015	61493	62866	cpxA	0/0	100.0	99.0	BA000007.3:4905062-4903688	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	aminocoumarin, aminoglycoside
contig00011	15387	16019	CRP	0/0	100.0	99.4	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00010	63505	64380	CTX-M-15	0/0	100.0	100.0	AY044436:1435-2311	CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family	cephalosporin
contig00063	6	503	dfrA12	0/0	100.0	100.0	GU585907.1:22103-21605	dfrA12 is an integron-encoded dihydrofolate reductase found in Vibrio cholerae	diaminopyrimidine
contig00002	58458	59630	emrA	0/0	100.0	100.0	AP009048:2810082-2811255	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	fluoroquinolone
contig00002	59647	61185	emrB	0/0	100.0	100.0	U00096:2812615-2814154	emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin.	fluoroquinolone
contig00014	121400	122455	emrK	0/0	100.0	99.9	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00002	57801	58331	emrR	0/0	100.0	99.8	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00014	119862	121400	emrY	0/0	100.0	99.9	D78168:1591-3130	emrY is a multidrug transport that moves substrates across the inner membrane of the Gram-negative E. coli. It is a homolog of emrB.	tetracycline
contig00010	131592	133235	eptA	0/0	100.0	99.9	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00008	37817	39010	Escherichia_coli_acrA	0/0	100.0	100.0	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00010	36337	37470	Escherichia_coli_ampC	0/0	100.0	97.3	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00009	106154	107458	Escherichia_coli_ampC1_beta-lactamase	0/0	100.0	99.9	FN649414.1:2765050-2766355	An ampC-like beta-lactamase identified from Escherichia coli.	cephalosporin, penam
contig00008	127045	128202	Escherichia_coli_ampH	0/0	100.0	100.0	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig00004	10013	11245	Escherichia_coli_mdfA	0/0	100.0	98.4	JQ394987:0-1233	Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter.	benzalkonium_chloride, rhodamine, tetracycline
contig00014	122978	123592	evgA	0/0	100.0	100.0	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00014	123597	127190	evgS	0/0	100.0	100.0	U00096:2484373-2487967	EvgS is a sensor protein that phosphorylates the regulatory protein EvgA. evgS corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	fluoroquinolone, macrolide, penam, tetracycline
contig00034	1783	2511	gadW	0/0	100.0	94.7	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig00034	592	1416	gadX	0/0	100.0	100.0	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00024	62969	63382	H-NS	0/0	100.0	99.3	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00016	8068	8745	kdpE	0/0	100.0	100.0	U00096.3:721733-721055	kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding.	aminoglycoside
contig00001	231041	231424	marA	0/0	100.0	100.0	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00033	40796	42043	mdtA	0/0	100.0	98.0	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00033	37674	40796	mdtB	0/0	100.0	99.8	U00096:2155262-2158385	MdtB is a transporter that forms a heteromultimer complex with MdtC to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex.	aminocoumarin
contig00033	34596	37673	mdtC	0/0	100.0	99.9	U00096:2158385-2161463	MdtC is a transporter that forms a heteromultimer complex with MdtB to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex. In the absence of MdtB MdtC can form a homomultimer complex that results in a functioning efflux complex with a narrower drug specificity. mdtC corresponds to 3 loci in Pseudomonas aeruginosa PAO1 (gene name: muxC/muxB) and 3 loci in Pseudomonas aeruginosa LESB58.	aminocoumarin
contig00034	6012	7169	mdtE	0/0	100.0	100.0	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00034	2874	5987	mdtF	0/0	100.0	100.0	U00096:3660413-3663527	MdtF is the multidrug inner membrane transporter for the MdtEF-TolC efflux complex.	fluoroquinolone, macrolide, penam
contig00018	16784	18010	mdtG	0/0	100.0	99.3	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00018	26639	27847	mdtH	0/0	100.0	100.0	U00096:1125326-1124117	Multidrug resistance protein MdtH	fluoroquinolone
contig00039	473	1684	mdtM	0/0	98.3	95.5	U00096.3:4568519-4567286	Multidrug resistance protein MdtM	acridine_dye, fluoroquinolone, lincosamide, nucleoside, phenicol
contig00031	10914	11945	mdtN	0/0	100.0	100.0	AP009048.1:4307588-4306556	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	acridine_dye, nucleoside
contig00031	11945	13996	mdtO	0/0	100.0	100.0	AP009048.1:4306557-4304505	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00031	13993	15459	mdtP	0/0	100.0	100.0	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00082	68	973	mphA	0/0	100.0	100.0	D16251.1:2531-1625	The mphA gene encodes for resistance enzyme MPH(2’)-I which preferentially inactivate 14-membered macrolides (e.g.erythromycin telithromycin roxithromycin) over 16-membered macrolides (e.g.tylosin spiramycin). It phosphorylates macrolides at 2’-OH hydroxyl of desosamine sugar of macrolides in a GTP-dependent manner.	macrolide
contig00009	50480	50956	mphB	0/0	100.0	98.3	AE005174.2:3397370-3397847	The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides.	macrolide
contig00004	92961	94709	msbA	0/0	100.0	100.0	U00096.3:966620-968369	MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability.	nitroimidazole
contig00014	17667	18635	pmrF	0/0	100.0	100.0	U00096:2367070-2368039	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide
contig00063	2207	3046	sul1	0/0	100.0	100.0	JF969163:1053-1893	Sul1 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria. It is linked to other resistance genes of class 1 integrons.	sulfonamide
contig00046	18447	19307	TEM-1	0/0	100.0	99.9	AL513383:161910-162771	TEM-1 is a broad-spectrum beta-lactamase found in many Gram-negative bacteria. Confers resistance to penicillins and first generation cephalosphorins.	cephalosporin, monobactam, penam, penem
contig00067	800	2005	tet(B)	0/0	100.0	99.8	AB089595:0-1206	Tet(B) is a tetracycline efflux protein expressed in many Gram-negative bacteria. It confers resistance to tetracycline doxycycline and minocycline but not tigecycline.	tetracycline
contig00003	196629	198116	tolC	0/0	100.0	99.7	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan
contig00013	42513	44156	yojI	0/0	100.0	100.0	U00096.3:2308615-2306971	YojI mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. YojI is capable of pumping out microcin molecules. The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI.	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00046	24279	25139	(AGly)aac3-IId	0/0	100	99.9	EU022314:1-861	(AGly)aac3-IId	NA
contig00063	923	1702	(AGly)aadA2	0/0	100	99.9	X68227:66-945	(AGly)aadA2	NA
contig00009	106154	107458	(Bla)AmpC1_Ecoli	0/0	100	99.9	FN649414:2765051-2766355	(Bla)AmpC1_Ecoli	NA
contig00010	36337	37470	(Bla)AmpC2_Ecoli	0/0	100	97.3	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00008	127045	128202	(Bla)ampH_Ecoli	0/0	100	100.0	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00010	63505	64380	(Bla)blaCTX-M-15	0/0	100	100.0	JQ686199:261-1136	(Bla)blaCTX-M-15	NA
contig00046	18447	19307	(Bla)blaTEM-105	0/0	100	99.9	AF516720:215-1075	(Bla)blaTEM-105	NA
contig00016	60155	62056	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100	100.0	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA
contig00082	68	973	(MLS)mph(A)	0/0	100	100.0	DQ445270:1626-2531	(MLS)mph(A)	NA
contig00060	5984	6643	(Phe)catA1	0/0	100	99.8	V00622:244-903	(Phe)catA1	NA
contig00063	2207	3046	(Sul)sul1	0/0	100	100.0	AF071413:6700-7539	(Sul)sul1	NA
contig00067	800	2005	(Tet)tetB	0/0	100	99.7	AB089594:1-1206	(Tet)tetB	NA
contig00063	6	503	(Tmt)dfrA12	0/0	100	100.0	Z21672:310-807	(Tmt)dfrA12	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00046	24279	25139	aac(3)-IId	0/0	100	100.0	NG_047251.1	aminoglycoside N-acetyltransferase AAC(3)-IId	GENTAMICIN
contig00063	911	1702	aadA2	0/0	100	100.0	NG_047343.1	ANT(3’’)-Ia family aminoglycoside nucleotidyltransferase AadA2	STREPTOMYCIN
contig00010	63505	64380	blaCTX-M-15	0/0	100	100.0	NG_048935.1	class A extended-spectrum beta-lactamase CTX-M-15	CEPHALOSPORIN
contig00010	36337	37470	blaEC-15	0/0	100	98.5	NG_049081.1	class C extended-spectrum beta-lactamase EC-15	CEPHALOSPORIN
contig00046	18447	19307	blaTEM-1	0/0	100	100.0	NG_050145.1	class A broad-spectrum beta-lactamase TEM-1	BETA-LACTAM
contig00060	5984	6643	catA1	0/0	100	99.8	NG_047582.1	type A-1 chloramphenicol O-acetyltransferase	CHLORAMPHENICOL
contig00063	6	503	dfrA12	0/0	100	100.0	NG_047689.1	trimethoprim-resistant dihydrofolate reductase DfrA12	TRIMETHOPRIM
contig00082	68	989	mph(A)	1/1	100	99.7	NG_047986.1	Mph(A) family macrolide 2’-phosphotransferase	MACROLIDE
contig00063	2207	3046	sul1	0/0	100	100.0	NG_048082.1	sulfonamide-resistant dihydropteroate synthase Sul1	SULFONAMIDE
contig00067	800	2005	tet(B)	0/0	100	100.0	NG_048163.1	tetracycline efflux MFS transporter Tet(B)	TETRACYCLINE

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00046	24279	25139	AAC3	0/0	100.0	100.0	MEG_64	Drugs:Aminoglycosides:Aminoglycoside_N-acetyltransferases:AAC3	NA
contig00008	37817	39010	ACRA	0/0	100.0	100.0	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00008	39033	42182	ACRB	0/0	100.0	100.0	MEG_401	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRB	NA
contig00009	71642	74755	ACRD	0/0	100.0	100.0	MEG_407	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ACRD	NA
contig00040	8641	9798	ACRE	0/0	100.0	99.9	MEG_408	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRE	NA
contig00040	5525	8629	ACRF	0/0	100.0	99.9	MEG_409	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRF	NA
contig00040	10197	10859	ACRS	0/0	100.0	100.0	MEG_415	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS	NA
contig00008	127045	128202	AMPH	0/0	100.0	100.0	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00063	901	1702	ANT3-DPRIME	0/0	97.9	99.9	MEG_975	Drugs:Aminoglycosides:Aminoglycoside_O-nucleotidyltransferases:ANT3-DPRIME	NA
contig00006	187571	189423	ASMA	0/0	100.0	97.2	MEG_1180	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:ASMA	NA
contig00003	220493	221314	BACA	0/0	100.0	98.9	MEG_1189	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00033	31061	31783	BAER	0/0	100.0	99.5	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00033	31780	33183	BAES	0/0	100.0	99.9	MEG_1193	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES	NA
contig00013	69768	70958	BCR	0/0	100.0	99.9	MEG_1210	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR	NA
contig00010	36337	37470	BLAEC	0/0	100.0	98.5	MEG_1282	Drugs:betalactams:Class_C_betalactamases:BLAEC	NA
contig00060	5984	6648	CATA	0/0	99.1	100.0	MEG_1593	Drugs:Phenicol:Chloramphenicol_acetyltransferases:CATA	NA
contig00015	60798	61496	CPXAR	0/0	100.0	100.0	MEG_2122	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00015	61493	62866	CPXAR	0/0	100.0	100.0	MEG_2121	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00011	15387	16019	CRP	0/0	100.0	99.4	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00055	12903	13845	CTX	0/0	100.0	98.2	MEG_2435	Drugs:betalactams:Class_A_betalactamases:CTX	NA
contig00063	6	503	DFRA	0/0	100.0	100.0	MEG_2551	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00002	58458	59630	EMRA	0/0	100.0	100.0	MEG_2722	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA	NA
contig00002	59647	61185	EMRB	0/0	100.0	100.0	MEG_2725	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRB	NA
contig00007	87250	88440	EMRD	0/0	100.0	100.0	MEG_2729	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD	NA
contig00014	121400	122563	EMRK	0/0	100.0	99.9	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig00002	57801	58331	EMRR	0/0	100.0	99.8	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00014	119862	121400	EMRY	0/0	100.0	99.9	MEG_2736	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRY	NA
contig00010	131592	133235	EPTA	0/0	100.0	99.9	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig00014	123597	127190	EVGS	0/0	100.0	100.0	MEG_2870	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EVGS	NA
contig00034	1783	2511	GADW	0/0	100.0	100.0	MEG_3081	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig00034	592	1416	GADX	0/0	100.0	100.0	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00024	62969	63382	HNS	0/0	100.0	99.3	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00016	8068	8745	KDPE	0/0	100.0	100.0	MEG_3448	Drugs:Aminoglycosides:Aminoglycoside_efflux_pumps:KDPE	NA
contig00001	231041	231430	MARA	0/0	100.0	100.0	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00001	231444	231878	MARR	0/0	100.0	100.0	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00004	10013	11245	MDFA	0/0	100.0	100.0	MEG_3737	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDFA	NA
contig00033	40796	42043	MDTA	0/0	100.0	98.0	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00033	37674	40796	MDTB	0/0	100.0	99.8	MEG_3747	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTB	NA
contig00033	34596	37673	MDTC	0/0	100.0	99.9	MEG_3749	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTC	NA
contig00034	6012	7169	MDTE	0/0	100.0	100.0	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00034	2874	5987	MDTF	0/0	100.0	100.0	MEG_3752	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTF	NA
contig00018	16784	18010	MDTG	0/0	100.0	99.9	MEG_3753	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig00018	26639	27847	MDTH	0/0	100.0	100.0	MEG_3755	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTH	NA
contig00001	198307	198636	MDTI	0/0	100.0	100.0	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00001	197955	198320	MDTJ	0/0	100.0	99.5	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00001	126553	127926	MDTK	0/0	100.0	100.0	MEG_3759	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:MDTK	NA
contig00039	473	1684	MDTM	0/0	98.3	95.5	MEG_3761	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTM	NA
contig00031	10914	11945	MDTN	0/0	100.0	100.0	MEG_3763	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN	NA
contig00031	11945	13996	MDTO	0/0	100.0	100.0	MEG_3764	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTO	NA
contig00031	13993	15459	MDTP	0/0	100.0	100.0	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig00082	68	989	MPHA	1/1	100.0	99.7	MEG_4030	Drugs:MLS:Macrolide_phosphotransferases:MPHA	NA
contig00009	50480	50956	MPHB	0/0	100.0	98.3	MEG_4033	Drugs:MLS:Macrolide_phosphotransferases:MPHB	NA
contig00004	92961	94709	MSBA	0/0	100.0	100.0	MEG_4061	Drugs:Multi-drug_resistance:Multi-drug_ABC_efflux_pumps:MSBA	NA
contig00016	60155	62056	PBP2	0/0	100.0	100.0	MEG_5400	Drugs:betalactams:Penicillin_binding_protein:PBP2	NA
contig00009	106154	107458	PBP4B	0/0	100.0	99.9	MEG_5409	Drugs:betalactams:Penicillin_binding_protein:PBP4B	NA
contig00014	17667	18635	PMRF	0/0	100.0	100.0	MEG_5801	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF	NA
contig00005	38665	39534	ROBA	0/0	100.0	99.0	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00031	37076	37399	SOXS	0/0	100.0	100.0	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00063	2206	3173	SULI	0/0	100.0	100.0	MEG_6615	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULI	NA
contig00067	800	2005	TETB	0/0	100.0	100.0	MEG_7052	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETB	NA
contig00067	2799	3215	TETD	0/0	100.0	100.0	MEG_7070	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETD	NA
contig00013	42513	44156	YOGI	0/0	100.0	100.0	MEG_7842	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:YOGI	NA

ID027

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00060	1221	2081	aac(3)-IId_1	0/0	100.0	99.9	EU022314	aac(3)-IId	Gentamicin, Tobramycin
contig00066	890	1678	aadA5_1	0/0	100.0	100.0	AF137361	aadA5	Streptomycin
contig00069	971	1774	aph(3’’)-Ib_5	0/0	100.0	100.0	AF321551	aph(3’’)-Ib	Streptomycin
contig00069	135	971	aph(6)-Id_1	0/0	100.0	99.9	M28829	aph(6)-Id	Streptomycin
contig00012	106601	107476	blaCTX-M-15_1	0/0	100.0	100.0	AY044436	blaCTX-M-15	Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig00057	142	1002	blaTEM-1B_1	0/0	100.0	100.0	AY458016	blaTEM-1B	Amoxicillin, Ampicillin, Cephalothin, Piperacillin, Ticarcillin
contig00066	1809	2282	dfrA17_1	0/0	100.0	100.0	FJ460238	dfrA17	Trimethoprim
contig00006	30138	31370	mdf(A)_1	0/0	100.0	99.9	Y08743	mdf(A)
contig00091	69	990	mph(A)_2	1/1	100.0	99.7	U36578	mph(A)	Erythromycin, Azithromycin, Spiramycin, Telithromycin
contig00069	1835	2650	sul2_2	0/0	100.0	100.0	AY034138	sul2	Sulfamethoxazole
contig00065	781	2027	tet(A)_6	0/0	97.8	100.0	AF534183	tet(A)	Doxycycline, Tetracycline

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00060	1221	2081	AAC(3)-IId	0/0	100.0	99.9	EU022314.1:0-861	AAC(3)-IId is a plasmid-encoded aminoglycoside acetyltransferase in E. coli	aminoglycoside
contig00066	890	1678	aadA5	0/0	100.0	100.0	AF137361:63-852	aadA5 is an aminoglycoside nucleotidyltransferase gene encoded by plasmids transposons and integrons in E. coli K. pneumoniae Kluyvera georgiana P. aeruginosa and E. cloacae	aminoglycoside
contig00003	39492	42641	acrB	0/0	100.0	100.0	U00096.3:484403-481253	Protein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug/proton antiporter.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00025	38165	41278	acrD	0/0	100.0	100.0	AP009048.1:2586250-2589364	AcrD is an aminoglycoside efflux pump expressed in E. coli. Its expression can be induced by indole and is regulated by baeRS and cpxAR.	aminoglycoside
contig00010	144794	145951	acrE	0/0	100.0	100.0	U00096:3413863-3415021	AcrE is a membrane fusion protein similar to AcrA.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00010	145963	149067	acrF	0/0	100.0	100.0	U00096:3415032-3418137	AcrF is a inner membrane transporter similar to AcrB.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00010	143733	144395	acrS	0/0	100.0	99.8	U00096:3413465-3412802	AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.	cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00069	971	1774	APH(3’’)-Ib	0/0	100.0	99.8	AF313472:15593-16397	APH(3’’)-Ib is an aminoglycoside phosphotransferase encoded by plasmids transposons integrative conjugative elements and chromosomes in Enterobacteriaceae and Pseudomonas spp.	aminoglycoside
contig00069	135	971	APH(6)-Id	0/0	100.0	99.8	AF024602:3155-3992	APH(6)-Id is an aminoglycoside phosphotransferase encoded by plasmids integrative conjugative elements and chromosomal genomic islands in K. pneumoniae Salmonella spp. E. coli Shigella flexneri Providencia alcalifaciens Pseudomonas spp. V. cholerae Edwardsiella tarda Pasteurella multocida and Aeromonas bestiarum	aminoglycoside
contig00002	178973	179794	bacA	0/0	100.0	100.0	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00017	62224	62946	baeR	0/0	100.0	100.0	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00017	62943	64346	baeS	0/0	100.0	100.0	AP009048:2165012-2166416	BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.	aminocoumarin, aminoglycoside
contig00014	61323	62696	cpxA	0/0	100.0	99.0	BA000007.3:4905062-4903688	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	aminocoumarin, aminoglycoside
contig00007	46838	47470	CRP	0/0	100.0	99.8	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00012	106601	107476	CTX-M-15	0/0	100.0	100.0	AY044436:1435-2311	CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family	cephalosporin
contig00066	1809	2282	dfrA17	0/0	100.0	100.0	DQ838665:0-474	dfrA17 is an integron-encoded dihydrofolate reductase found in Escherichia coli	diaminopyrimidine
contig00011	70596	71768	emrA	0/0	100.0	100.0	AP009048:2810082-2811255	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	fluoroquinolone
contig00011	71785	73323	emrB	0/0	100.0	100.0	U00096:2812615-2814154	emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin.	fluoroquinolone
contig00001	241167	242222	emrK	0/0	100.0	100.0	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00011	69939	70469	emrR	0/0	100.0	100.0	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00001	239629	241167	emrY	0/0	100.0	99.9	D78168:1591-3130	emrY is a multidrug transport that moves substrates across the inner membrane of the Gram-negative E. coli. It is a homolog of emrB.	tetracycline
contig00013	8050	9693	eptA	0/0	100.0	100.0	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00003	38276	39469	Escherichia_coli_acrA	0/0	100.0	100.0	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00008	142575	143708	Escherichia_coli_ampC	0/0	100.0	100.0	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00025	72676	73980	Escherichia_coli_ampC1_beta-lactamase	0/0	100.0	99.4	FN649414.1:2765050-2766355	An ampC-like beta-lactamase identified from Escherichia coli.	cephalosporin, penam
contig00003	127608	128765	Escherichia_coli_ampH	0/0	100.0	100.0	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig00043	15224	15556	Escherichia_coli_emrE	0/0	100.0	91.9	Z11877.1:485-818	Member of the small MDR (multidrug resistance) family of transporters, in Escherichia coli this protein provides resistance against a number of positively charged compounds including ethidium bromide and erythromycin, proton-dependent secondary transporter which exchanges protons for compound translocation	macrolide
contig00006	30138	31370	Escherichia_coli_mdfA	0/0	100.0	98.4	JQ394987:0-1233	Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter.	benzalkonium_chloride, rhodamine, tetracycline
contig00001	242745	243359	evgA	0/0	100.0	100.0	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00001	243364	246957	evgS	0/0	100.0	100.0	U00096:2484373-2487967	EvgS is a sensor protein that phosphorylates the regulatory protein EvgA. evgS corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	fluoroquinolone, macrolide, penam, tetracycline
contig00038	40033	40761	gadW	0/0	100.0	94.7	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig00038	41129	41953	gadX	0/0	100.0	99.9	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00009	154764	155177	H-NS	0/0	100.0	99.3	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00015	8068	8745	kdpE	0/0	100.0	100.0	U00096.3:721733-721055	kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding.	aminoglycoside
contig00031	47771	48154	marA	0/0	100.0	100.0	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00017	71959	73206	mdtA	0/0	100.0	98.0	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00017	68837	71959	mdtB	0/0	100.0	99.0	U00096:2155262-2158385	MdtB is a transporter that forms a heteromultimer complex with MdtC to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex.	aminocoumarin
contig00017	65759	68836	mdtC	0/0	100.0	99.8	U00096:2158385-2161463	MdtC is a transporter that forms a heteromultimer complex with MdtB to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex. In the absence of MdtB MdtC can form a homomultimer complex that results in a functioning efflux complex with a narrower drug specificity. mdtC corresponds to 3 loci in Pseudomonas aeruginosa PAO1 (gene name: muxC/muxB) and 3 loci in Pseudomonas aeruginosa LESB58.	aminocoumarin
contig00038	35375	36532	mdtE	0/0	100.0	100.0	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00038	36557	39670	mdtF	0/0	100.0	100.0	U00096:3660413-3663527	MdtF is the multidrug inner membrane transporter for the MdtEF-TolC efflux complex.	fluoroquinolone, macrolide, penam
contig00016	18398	19624	mdtG	0/0	100.0	99.4	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00016	28253	29461	mdtH	0/0	100.0	100.0	U00096:1125326-1124117	Multidrug resistance protein MdtH	fluoroquinolone
contig00051	461	1672	mdtM	0/0	98.3	95.5	U00096.3:4568519-4567286	Multidrug resistance protein MdtM	acridine_dye, fluoroquinolone, lincosamide, nucleoside, phenicol
contig00013	39131	40162	mdtN	0/0	100.0	100.0	AP009048.1:4307588-4306556	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	acridine_dye, nucleoside
contig00013	40162	42213	mdtO	0/0	100.0	99.9	AP009048.1:4306557-4304505	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00013	42210	43676	mdtP	0/0	100.0	100.0	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00091	69	974	mphA	0/0	100.0	100.0	D16251.1:2531-1625	The mphA gene encodes for resistance enzyme MPH(2’)-I which preferentially inactivate 14-membered macrolides (e.g.erythromycin telithromycin roxithromycin) over 16-membered macrolides (e.g.tylosin spiramycin). It phosphorylates macrolides at 2’-OH hydroxyl of desosamine sugar of macrolides in a GTP-dependent manner.	macrolide
contig00025	17003	17479	mphB	0/0	100.0	98.3	AE005174.2:3397370-3397847	The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides.	macrolide
contig00026	51528	53276	msbA	0/0	100.0	100.0	U00096.3:966620-968369	MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability.	nitroimidazole
contig00001	136313	137281	pmrF	0/0	100.0	100.0	U00096:2367070-2368039	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide
contig00069	1835	2650	sul2	0/0	100.0	100.0	AY055428.1:21084-20268	Sul2 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria usually found on small plasmids.	sulfonamide
contig00057	142	1002	TEM-1	0/0	100.0	99.9	AL513383:161910-162771	TEM-1 is a broad-spectrum beta-lactamase found in many Gram-negative bacteria. Confers resistance to penicillins and first generation cephalosphorins.	cephalosporin, monobactam, penam, penem
contig00065	781	2027	tet(A)	0/0	97.8	100.0	AF534183.1:2970-4245	TetA is a tetracycline efflux pump found in many species of Gram-negative bacteria.	tetracycline
contig00002	155108	156595	tolC	0/0	100.0	100.0	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan
contig00001	76214	77857	yojI	0/0	100.0	100.0	U00096.3:2308615-2306971	YojI mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. YojI is capable of pumping out microcin molecules. The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI.	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00060	1221	2081	(AGly)aac3-IId	0/0	100.0	99.9	EU022314:1-861	(AGly)aac3-IId	NA
contig00066	890	1678	(AGly)aadA5	0/0	100.0	100.0	AF137361:64-852	(AGly)aadA5	NA
contig00069	971	1774	(AGly)strA	0/0	100.0	99.9	AB366441:22458-23261	(AGly)strA	NA
contig00069	135	971	(AGly)strB	0/0	100.0	99.9	FJ474091:264-1100	(AGly)strB	NA
contig00025	72676	73980	(Bla)AmpC1_Ecoli	0/0	100.0	99.4	FN649414:2765051-2766355	(Bla)AmpC1_Ecoli	NA
contig00008	142575	143708	(Bla)AmpC2_Ecoli	0/0	100.0	100.0	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00003	127608	128765	(Bla)ampH_Ecoli	0/0	100.0	100.0	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00012	106601	107476	(Bla)blaCTX-M-15	0/0	100.0	100.0	JQ686199:261-1136	(Bla)blaCTX-M-15	NA
contig00057	142	1002	(Bla)blaTEM-105	0/0	100.0	99.9	AF516720:215-1075	(Bla)blaTEM-105	NA
contig00015	60385	62286	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100.0	100.0	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA
contig00091	69	974	(MLS)mph(A)	0/0	100.0	100.0	DQ445270:1626-2531	(MLS)mph(A)	NA
contig00069	1835	2650	(Sul)sul2	0/0	100.0	100.0	EU360945:1617-2432	(Sul)sul2	NA
contig00065	781	2055	(Tet)tetA	0/0	100.0	100.0	JX424423:94438-95712	(Tet)tetA	NA
contig00065	124	750	(Tet)tetR	1/24	96.3	96.2	HF545434:53576-54226	(Tet)tetR	NA
contig00066	1809	2282	(Tmt)dfrA17	0/0	100.0	100.0	AB126604:98-571	(Tmt)dfrA17	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00060	1221	2081	aac(3)-IId	0/0	100	100.0	NG_047251.1	aminoglycoside N-acetyltransferase AAC(3)-IId	GENTAMICIN
contig00066	890	1678	aadA5	0/0	100	100.0	NG_047357.1	ANT(3’’)-Ia family aminoglycoside nucleotidyltransferase AadA5	STREPTOMYCIN
contig00069	971	1798	aph(3’’)-Ib	0/0	100	100.0	NG_056002.2	aminoglycoside O-phosphotransferase APH(3’’)-Ib	STREPTOMYCIN
contig00069	135	971	aph(6)-Id	0/0	100	100.0	NG_047466.1	aminoglycoside O-phosphotransferase APH(6)-Id	STREPTOMYCIN
contig00012	106601	107476	blaCTX-M-15	0/0	100	100.0	NG_048935.1	class A extended-spectrum beta-lactamase CTX-M-15	CEPHALOSPORIN
contig00008	142575	143708	blaEC	0/0	100	100.0	NG_047494.1	BlaEC family class C beta-lactamase	BETA-LACTAM
contig00057	142	1002	blaTEM-1	0/0	100	100.0	NG_050145.1	class A broad-spectrum beta-lactamase TEM-1	BETA-LACTAM
contig00066	1809	2282	dfrA17	0/0	100	99.8	NG_047710.1	trimethoprim-resistant dihydrofolate reductase DfrA17	TRIMETHOPRIM
contig00091	69	990	mph(A)	1/1	100	99.7	NG_047986.1	Mph(A) family macrolide 2’-phosphotransferase	MACROLIDE
contig00069	1835	2650	sul2	0/0	100	100.0	NG_051852.1	sulfonamide-resistant dihydropteroate synthase Sul2	SULFONAMIDE
contig00065	856	2055	tet(A)	0/0	100	100.0	NG_048154.1	tetracycline efflux MFS transporter Tet(A)	TETRACYCLINE

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00060	1221	2081	AAC3	0/0	100.0	100.0	MEG_64	Drugs:Aminoglycosides:Aminoglycoside_N-acetyltransferases:AAC3	NA
contig00003	38276	39469	ACRA	0/0	100.0	100.0	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00003	39492	42641	ACRB	0/0	100.0	100.0	MEG_401	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRB	NA
contig00025	38165	41278	ACRD	0/0	100.0	100.0	MEG_407	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ACRD	NA
contig00010	144794	145951	ACRE	0/0	100.0	100.0	MEG_408	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRE	NA
contig00010	145963	149067	ACRF	0/0	100.0	100.0	MEG_409	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRF	NA
contig00010	143733	144395	ACRS	0/0	100.0	99.8	MEG_415	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS	NA
contig00008	142575	143708	AMPC	0/0	100.0	100.0	MEG_728	Drugs:betalactams:Class_C_betalactamases:AMPC	NA
contig00003	127608	128765	AMPH	0/0	100.0	100.0	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00066	890	1678	ANT3-DPRIME	0/0	100.0	100.0	MEG_928	Drugs:Aminoglycosides:Aminoglycoside_O-nucleotidyltransferases:ANT3-DPRIME	NA
contig00069	971	1798	APH3-DPRIME	0/0	100.0	100.0	MEG_1019	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH3-DPRIME	NA
contig00069	135	971	APH6	0/0	100.0	100.0	MEG_1084	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH6	NA
contig00017	84817	86669	ASMA	0/0	100.0	97.5	MEG_1180	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:ASMA	NA
contig00002	178973	179794	BACA	0/0	100.0	100.0	MEG_1190	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00017	62224	62946	BAER	0/0	100.0	100.0	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00017	62943	64346	BAES	0/0	100.0	100.0	MEG_1193	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES	NA
contig00001	49237	50427	BCR	0/0	100.0	100.0	MEG_1210	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR	NA
contig00014	60628	61326	CPXAR	0/0	100.0	100.0	MEG_2122	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00014	61323	62696	CPXAR	0/0	100.0	100.0	MEG_2121	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00007	46838	47470	CRP	0/0	100.0	99.8	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00066	1809	2282	DFRA	0/0	100.0	100.0	MEG_2547	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00011	70596	71768	EMRA	0/0	100.0	100.0	MEG_2722	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA	NA
contig00011	71785	73323	EMRB	0/0	100.0	100.0	MEG_2725	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRB	NA
contig00018	21891	23081	EMRD	0/0	100.0	99.9	MEG_2729	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD	NA
contig00001	241167	242330	EMRK	0/0	100.0	100.0	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig00011	69939	70469	EMRR	0/0	100.0	100.0	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00001	239629	241167	EMRY	0/0	100.0	100.0	MEG_2736	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRY	NA
contig00013	8050	9693	EPTA	0/0	100.0	100.0	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig00001	243364	246957	EVGS	0/0	100.0	100.0	MEG_2870	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EVGS	NA
contig00038	40033	40761	GADW	0/0	100.0	100.0	MEG_3081	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig00038	41129	41953	GADX	0/0	100.0	99.9	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00009	154764	155177	HNS	0/0	100.0	99.3	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00015	8068	8745	KDPE	0/0	100.0	100.0	MEG_3448	Drugs:Aminoglycosides:Aminoglycoside_efflux_pumps:KDPE	NA
contig00031	47765	48154	MARA	0/0	100.0	100.0	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00031	47317	47751	MARR	0/0	100.0	100.0	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00006	30138	31370	MDFA	0/0	100.0	100.0	MEG_3737	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDFA	NA
contig00017	71959	73206	MDTA	0/0	100.0	98.0	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00017	68837	71959	MDTB	0/0	100.0	99.0	MEG_3747	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTB	NA
contig00017	65759	68836	MDTC	0/0	100.0	99.8	MEG_3749	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTC	NA
contig00038	35375	36532	MDTE	0/0	100.0	100.0	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00038	36557	39670	MDTF	0/0	100.0	100.0	MEG_3752	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTF	NA
contig00016	18398	19624	MDTG	0/0	100.0	100.0	MEG_3753	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig00016	28253	29461	MDTH	0/0	100.0	100.0	MEG_3755	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTH	NA
contig00037	23235	23564	MDTI	0/0	100.0	100.0	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00037	23551	23916	MDTJ	0/0	100.0	99.5	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00005	135264	136637	MDTK	0/0	100.0	100.0	MEG_3759	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:MDTK	NA
contig00051	461	1672	MDTM	0/0	98.3	95.5	MEG_3761	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTM	NA
contig00013	39131	40162	MDTN	0/0	100.0	100.0	MEG_3763	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN	NA
contig00013	40162	42213	MDTO	0/0	100.0	99.9	MEG_3764	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTO	NA
contig00013	42210	43676	MDTP	0/0	100.0	100.0	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig00091	69	990	MPHA	1/1	100.0	99.7	MEG_4030	Drugs:MLS:Macrolide_phosphotransferases:MPHA	NA
contig00025	17003	17479	MPHB	0/0	100.0	98.3	MEG_4033	Drugs:MLS:Macrolide_phosphotransferases:MPHB	NA
contig00026	51528	53276	MSBA	0/0	100.0	100.0	MEG_4061	Drugs:Multi-drug_resistance:Multi-drug_ABC_efflux_pumps:MSBA	NA
contig00043	15224	15556	MVRC	0/0	100.0	91.9	MEG_4103	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MVRC	NA
contig00015	60385	62286	PBP2	0/0	100.0	100.0	MEG_5400	Drugs:betalactams:Penicillin_binding_protein:PBP2	NA
contig00025	72676	73980	PBP4B	0/0	100.0	99.4	MEG_5409	Drugs:betalactams:Penicillin_binding_protein:PBP4B	NA
contig00001	136313	137281	PMRF	0/0	100.0	100.0	MEG_5801	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF	NA
contig00028	21718	22587	ROBA	0/0	100.0	99.0	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00013	65745	66068	SOXS	0/0	100.0	100.0	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00069	1835	2650	SULII	0/0	100.0	100.0	MEG_6617	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULII	NA
contig00065	781	2055	TETA	0/0	100.0	100.0	MEG_7024	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETA	NA
contig00001	76214	77857	YOGI	0/0	100.0	100.0	MEG_7842	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:YOGI	NA

ID031

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00090	8412	9272	aac(3)-IId_1	0/0	100.0	99.9	EU022314	aac(3)-IId	Gentamicin, Tobramycin
contig00096	1399	2200	aadA2_1	0/0	97.9	99.9	NC_010870	aadA2	Streptomycin
contig00109	5465	6244	aph(3’’)-Ib_5	0/0	97.0	100.0	AF321551	aph(3’’)-Ib	Streptomycin
contig00109	4629	5465	aph(6)-Id_1	0/0	100.0	100.0	M28829	aph(6)-Id	Streptomycin
contig00087	6962	7837	blaCTX-M-15_1	0/0	100.0	100.0	AY044436	blaCTX-M-15	Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig00090	2580	3440	blaTEM-1B_1	0/0	100.0	100.0	AY458016	blaTEM-1B	Amoxicillin, Ampicillin, Cephalothin, Piperacillin, Ticarcillin
contig00122	222	881	catA1_1	0/0	100.0	99.8	V00622	catA1	Chloramphenicol
contig00096	504	1001	dfrA12_8	0/0	100.0	100.0	AM040708	dfrA12	Trimethoprim
contig00010	65054	66286	mdf(A)_1	0/0	100.0	99.9	Y08743	mdf(A)
contig00161	69	962	mph(A)_1	0/0	98.7	100.0	D16251	mph(A)	Erythromycin, Azithromycin, Spiramycin, Telithromycin
contig00096	2678	3544	sul1_5	0/0	100.0	99.9	EU780013	sul1	Sulfamethoxazole
contig00109	85	900	sul2_2	0/0	100.0	100.0	AY034138	sul2	Sulfamethoxazole
contig00115	1570	2775	tet(B)_2	0/0	100.0	100.0	AF326777	tet(B)	Doxycycline, Tetracycline, Minocycline

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00090	8412	9272	AAC(3)-IId	0/0	100.0	99.9	EU022314.1:0-861	AAC(3)-IId is a plasmid-encoded aminoglycoside acetyltransferase in E. coli	aminoglycoside
contig00096	1421	2200	aadA2	0/0	100.0	99.9	AF156486:5012-5792	aadA2 is an aminoglycoside nucleotidyltransferase gene encoded by plasmids and integrons in K. pneumoniae Salmonella spp. Corynebacterium glutamicum C. freundii and Aeromonas spp.	aminoglycoside
contig00005	38857	42006	acrB	0/0	100.0	100.0	U00096.3:484403-481253	Protein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug/proton antiporter.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00002	181007	184120	acrD	0/0	100.0	100.0	AP009048.1:2586250-2589364	AcrD is an aminoglycoside efflux pump expressed in E. coli. Its expression can be induced by indole and is regulated by baeRS and cpxAR.	aminoglycoside
contig00051	8641	9798	acrE	0/0	100.0	100.0	U00096:3413863-3415021	AcrE is a membrane fusion protein similar to AcrA.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00051	5525	8629	acrF	0/0	100.0	99.4	U00096:3415032-3418137	AcrF is a inner membrane transporter similar to AcrB.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00051	10197	10859	acrS	0/0	100.0	100.0	U00096:3413465-3412802	AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.	cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00109	5465	6244	APH(3’’)-Ib	0/0	97.0	99.7	AF313472:15593-16397	APH(3’’)-Ib is an aminoglycoside phosphotransferase encoded by plasmids transposons integrative conjugative elements and chromosomes in Enterobacteriaceae and Pseudomonas spp.	aminoglycoside
contig00109	4629	5465	APH(6)-Id	0/0	100.0	99.9	AF024602:3155-3992	APH(6)-Id is an aminoglycoside phosphotransferase encoded by plasmids integrative conjugative elements and chromosomal genomic islands in K. pneumoniae Salmonella spp. E. coli Shigella flexneri Providencia alcalifaciens Pseudomonas spp. V. cholerae Edwardsiella tarda Pasteurella multocida and Aeromonas bestiarum	aminoglycoside
contig00079	10387	11208	bacA	0/0	100.0	100.0	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00020	13325	14047	baeR	0/0	100.0	100.0	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00020	11925	13328	baeS	0/0	100.0	99.9	AP009048:2165012-2166416	BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.	aminocoumarin, aminoglycoside
contig00122	222	881	catI	0/0	100.0	99.8	V00622:243-903	catI is a chromosome and transposon-encoded variant of the cat gene found in Escherichia coli and Acinetobacter baumannii	phenicol
contig00012	61495	62868	cpxA	0/0	100.0	99.0	BA000007.3:4905062-4903688	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	aminocoumarin, aminoglycoside
contig00019	15936	16568	CRP	0/0	100.0	99.4	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00087	6962	7837	CTX-M-15	0/0	100.0	100.0	AY044436:1435-2311	CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family	cephalosporin
contig00096	504	1001	dfrA12	0/0	100.0	100.0	GU585907.1:22103-21605	dfrA12 is an integron-encoded dihydrofolate reductase found in Vibrio cholerae	diaminopyrimidine
contig00001	19882	21054	emrA	0/0	100.0	99.7	AP009048:2810082-2811255	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	fluoroquinolone
contig00001	21071	22609	emrB	0/0	100.0	99.9	U00096:2812615-2814154	emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin.	fluoroquinolone
contig00002	83737	84792	emrK	0/0	100.0	99.9	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00001	19225	19755	emrR	0/0	100.0	100.0	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00002	82199	83737	emrY	0/0	100.0	99.0	D78168:1591-3130	emrY is a multidrug transport that moves substrates across the inner membrane of the Gram-negative E. coli. It is a homolog of emrB.	tetracycline
contig00056	18707	20350	eptA	0/0	100.0	100.0	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00005	37641	38834	Escherichia_coli_acrA	0/0	100.0	100.0	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00003	139594	140727	Escherichia_coli_ampC	0/0	100.0	97.2	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00002	148304	149608	Escherichia_coli_ampC1_beta-lactamase	0/0	100.0	100.0	FN649414.1:2765050-2766355	An ampC-like beta-lactamase identified from Escherichia coli.	cephalosporin, penam
contig00005	126972	128129	Escherichia_coli_ampH	0/0	100.0	98.9	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig00010	65054	66286	Escherichia_coli_mdfA	0/0	100.0	98.4	JQ394987:0-1233	Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter.	benzalkonium_chloride, rhodamine, tetracycline
contig00002	85316	85930	evgA	0/0	100.0	100.0	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00002	85935	89528	evgS	0/0	100.0	99.7	U00096:2484373-2487967	EvgS is a sensor protein that phosphorylates the regulatory protein EvgA. evgS corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	fluoroquinolone, macrolide, penam, tetracycline
contig00028	25644	26372	gadW	0/0	100.0	94.7	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig00028	24452	25276	gadX	0/0	100.0	100.0	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00015	24206	24619	H-NS	0/0	100.0	99.5	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00036	8068	8745	kdpE	0/0	100.0	100.0	U00096.3:721733-721055	kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding.	aminoglycoside
contig00040	24456	24839	marA	0/0	100.0	99.7	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00020	3065	4312	mdtA	0/0	100.0	100.0	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00020	4312	7434	mdtB	0/0	100.0	99.8	U00096:2155262-2158385	MdtB is a transporter that forms a heteromultimer complex with MdtC to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex.	aminocoumarin
contig00020	7435	10512	mdtC	0/0	100.0	99.9	U00096:2158385-2161463	MdtC is a transporter that forms a heteromultimer complex with MdtB to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex. In the absence of MdtB MdtC can form a homomultimer complex that results in a functioning efflux complex with a narrower drug specificity. mdtC corresponds to 3 loci in Pseudomonas aeruginosa PAO1 (gene name: muxC/muxB) and 3 loci in Pseudomonas aeruginosa LESB58.	aminocoumarin
contig00028	29873	31030	mdtE	0/0	100.0	100.0	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00028	26735	29848	mdtF	0/0	100.0	100.0	U00096:3660413-3663527	MdtF is the multidrug inner membrane transporter for the MdtEF-TolC efflux complex.	fluoroquinolone, macrolide, penam
contig00008	82627	83853	mdtG	0/0	100.0	99.4	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00008	72791	73999	mdtH	0/0	100.0	99.8	U00096:1125326-1124117	Multidrug resistance protein MdtH	fluoroquinolone
contig00067	263	1474	mdtM	0/0	98.3	95.5	U00096.3:4568519-4567286	Multidrug resistance protein MdtM	acridine_dye, fluoroquinolone, lincosamide, nucleoside, phenicol
contig00043	2261	3292	mdtN	0/0	100.0	100.0	AP009048.1:4307588-4306556	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	acridine_dye, nucleoside
contig00043	3292	5343	mdtO	0/0	100.0	100.0	AP009048.1:4306557-4304505	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00043	5340	6806	mdtP	0/0	100.0	100.0	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00161	69	962	mphA	0/0	98.7	100.0	D16251.1:2531-1625	The mphA gene encodes for resistance enzyme MPH(2’)-I which preferentially inactivate 14-membered macrolides (e.g.erythromycin telithromycin roxithromycin) over 16-membered macrolides (e.g.tylosin spiramycin). It phosphorylates macrolides at 2’-OH hydroxyl of desosamine sugar of macrolides in a GTP-dependent manner.	macrolide
contig00007	9441	9915	mphB	0/0	99.6	97.3	AE005174.2:3397370-3397847	The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides.	macrolide
contig00016	51586	53334	msbA	0/0	100.0	100.0	U00096.3:966620-968369	MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability.	nitroimidazole
contig00004	14362	15330	pmrF	0/0	100.0	99.4	U00096:2367070-2368039	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide
contig00096	2705	3544	sul1	0/0	100.0	100.0	JF969163:1053-1893	Sul1 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria. It is linked to other resistance genes of class 1 integrons.	sulfonamide
contig00109	85	900	sul2	0/0	100.0	100.0	AY055428.1:21084-20268	Sul2 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria usually found on small plasmids.	sulfonamide
contig00090	2580	3440	TEM-1	0/0	100.0	99.9	AL513383:161910-162771	TEM-1 is a broad-spectrum beta-lactamase found in many Gram-negative bacteria. Confers resistance to penicillins and first generation cephalosphorins.	cephalosporin, monobactam, penam, penem
contig00115	1570	2775	tet(B)	0/0	100.0	99.8	AB089595:0-1206	Tet(B) is a tetracycline efflux protein expressed in many Gram-negative bacteria. It confers resistance to tetracycline doxycycline and minocycline but not tigecycline.	tetracycline
contig00026	43243	44730	tolC	0/0	100.0	99.7	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan
contig00004	62509	64152	yojI	0/0	100.0	98.1	U00096.3:2308615-2306971	YojI mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. YojI is capable of pumping out microcin molecules. The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI.	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00090	8412	9272	(AGly)aac3-IId	0/0	100.0	99.9	EU022314:1-861	(AGly)aac3-IId	NA
contig00096	1421	2200	(AGly)aadA2	0/0	100.0	99.9	X68227:66-945	(AGly)aadA2	NA
contig00109	5465	6244	(AGly)strA	0/0	97.0	99.9	AB366441:22458-23261	(AGly)strA	NA
contig00109	4629	5465	(AGly)strB	0/0	100.0	100.0	FJ474091:264-1100	(AGly)strB	NA
contig00002	148304	149608	(Bla)AmpC1_Ecoli	0/0	100.0	100.0	FN649414:2765051-2766355	(Bla)AmpC1_Ecoli	NA
contig00003	139594	140727	(Bla)AmpC2_Ecoli	0/0	100.0	97.2	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00005	126972	128129	(Bla)ampH_Ecoli	0/0	100.0	98.9	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00087	6962	7837	(Bla)blaCTX-M-15	0/0	100.0	100.0	JQ686199:261-1136	(Bla)blaCTX-M-15	NA
contig00090	2580	3440	(Bla)blaTEM-105	0/0	100.0	99.9	AF516720:215-1075	(Bla)blaTEM-105	NA
contig00021	14767	16668	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100.0	100.0	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA
contig00161	69	962	(MLS)mph(A)	0/0	98.7	100.0	DQ445270:1626-2531	(MLS)mph(A)	NA
contig00122	222	881	(Phe)catA1	0/0	100.0	99.8	V00622:244-903	(Phe)catA1	NA
contig00096	2705	3544	(Sul)sul1	0/0	100.0	100.0	AF071413:6700-7539	(Sul)sul1	NA
contig00109	85	900	(Sul)sul2	0/0	100.0	100.0	EU360945:1617-2432	(Sul)sul2	NA
contig00115	1570	2775	(Tet)tetB	0/0	100.0	99.7	AB089594:1-1206	(Tet)tetB	NA
contig00096	504	1001	(Tmt)dfrA12	0/0	100.0	100.0	Z21672:310-807	(Tmt)dfrA12	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00090	8412	9272	aac(3)-IId	0/0	100.0	100.0	NG_047251.1	aminoglycoside N-acetyltransferase AAC(3)-IId	GENTAMICIN
contig00096	1409	2200	aadA2	0/0	100.0	100.0	NG_047343.1	ANT(3’’)-Ia family aminoglycoside nucleotidyltransferase AadA2	STREPTOMYCIN
contig00109	5465	6244	aph(3’’)-Ib	0/0	94.2	100.0	NG_056002.2	aminoglycoside O-phosphotransferase APH(3’’)-Ib	STREPTOMYCIN
contig00109	4629	5465	aph(6)-Id	0/0	100.0	100.0	NG_047464.1	aminoglycoside O-phosphotransferase APH(6)-Id	STREPTOMYCIN
contig00087	6962	7837	blaCTX-M-15	0/0	100.0	100.0	NG_048935.1	class A extended-spectrum beta-lactamase CTX-M-15	CEPHALOSPORIN
contig00003	139594	140727	blaEC-15	0/0	100.0	98.4	NG_049081.1	class C extended-spectrum beta-lactamase EC-15	CEPHALOSPORIN
contig00090	2580	3440	blaTEM-1	0/0	100.0	100.0	NG_050145.1	class A broad-spectrum beta-lactamase TEM-1	BETA-LACTAM
contig00122	222	881	catA1	0/0	100.0	99.8	NG_047582.1	type A-1 chloramphenicol O-acetyltransferase	CHLORAMPHENICOL
contig00096	504	1001	dfrA12	0/0	100.0	100.0	NG_047689.1	trimethoprim-resistant dihydrofolate reductase DfrA12	TRIMETHOPRIM
contig00161	69	962	mph(A)	0/0	98.7	100.0	NG_047985.1	Mph(A) family macrolide 2’-phosphotransferase	MACROLIDE
contig00096	2705	3544	sul1	0/0	100.0	100.0	NG_048082.1	sulfonamide-resistant dihydropteroate synthase Sul1	SULFONAMIDE
contig00109	85	900	sul2	0/0	100.0	100.0	NG_051852.1	sulfonamide-resistant dihydropteroate synthase Sul2	SULFONAMIDE
contig00115	1570	2775	tet(B)	0/0	100.0	100.0	NG_048163.1	tetracycline efflux MFS transporter Tet(B)	TETRACYCLINE

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00090	8412	9272	AAC3	0/0	100.0	100.0	MEG_64	Drugs:Aminoglycosides:Aminoglycoside_N-acetyltransferases:AAC3	NA
contig00005	37641	38834	ACRA	0/0	100.0	100.0	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00005	38857	42006	ACRB	0/0	100.0	100.0	MEG_401	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRB	NA
contig00002	181007	184120	ACRD	0/0	100.0	100.0	MEG_407	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ACRD	NA
contig00051	8641	9798	ACRE	0/0	100.0	100.0	MEG_408	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRE	NA
contig00051	5525	8629	ACRF	0/0	100.0	99.4	MEG_409	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRF	NA
contig00051	10197	10859	ACRS	0/0	100.0	100.0	MEG_415	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS	NA
contig00005	126972	128129	AMPH	0/0	100.0	98.9	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00096	1399	2200	ANT3-DPRIME	0/0	97.9	99.9	MEG_975	Drugs:Aminoglycosides:Aminoglycoside_O-nucleotidyltransferases:ANT3-DPRIME	NA
contig00109	5465	6244	APH3-DPRIME	0/0	94.2	100.0	MEG_1019	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH3-DPRIME	NA
contig00109	4629	5465	APH6	0/0	100.0	100.0	MEG_1086	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH6	NA
contig00070	6721	8573	ASMA	0/0	100.0	98.1	MEG_1180	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:ASMA	NA
contig00079	10387	11208	BACA	0/0	100.0	100.0	MEG_1190	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00020	13325	14047	BAER	0/0	100.0	100.0	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00020	11925	13328	BAES	0/0	100.0	99.9	MEG_1193	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES	NA
contig00004	89654	90844	BCR	0/0	100.0	98.2	MEG_1210	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR	NA
contig00003	139594	140727	BLAEC	0/0	100.0	98.4	MEG_1282	Drugs:betalactams:Class_C_betalactamases:BLAEC	NA
contig00122	211	881	CATA	0/0	100.0	100.0	MEG_1593	Drugs:Phenicol:Chloramphenicol_acetyltransferases:CATA	NA
contig00012	60800	61498	CPXAR	0/0	100.0	99.9	MEG_2122	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00012	61495	62868	CPXAR	0/0	100.0	100.0	MEG_2121	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00019	15936	16568	CRP	0/0	100.0	99.4	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00106	5789	6731	CTX	0/0	100.0	97.0	MEG_2435	Drugs:betalactams:Class_A_betalactamases:CTX	NA
contig00096	504	1001	DFRA	0/0	100.0	100.0	MEG_2551	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00001	19882	21054	EMRA	0/0	100.0	99.7	MEG_2722	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA	NA
contig00001	21071	22609	EMRB	0/0	100.0	99.9	MEG_2725	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRB	NA
contig00078	9775	10965	EMRD	0/0	100.0	100.0	MEG_2729	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD	NA
contig00002	83737	84900	EMRK	0/0	100.0	99.9	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig00001	19225	19755	EMRR	0/0	100.0	100.0	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00002	82199	83737	EMRY	0/0	100.0	99.1	MEG_2736	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRY	NA
contig00056	18707	20350	EPTA	0/0	100.0	100.0	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig00002	85935	89528	EVGS	0/0	100.0	99.7	MEG_2870	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EVGS	NA
contig00028	25644	26372	GADW	0/0	100.0	100.0	MEG_3081	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig00028	24452	25276	GADX	0/0	100.0	100.0	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00015	24206	24619	HNS	0/0	100.0	99.5	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00036	8068	8745	KDPE	0/0	100.0	100.0	MEG_3448	Drugs:Aminoglycosides:Aminoglycoside_efflux_pumps:KDPE	NA
contig00040	24450	24839	MARA	0/0	100.0	99.7	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00040	24001	24435	MARR	0/0	100.0	98.4	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00010	65054	66286	MDFA	0/0	100.0	100.0	MEG_3737	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDFA	NA
contig00020	3065	4312	MDTA	0/0	100.0	100.0	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00020	4312	7434	MDTB	0/0	100.0	99.8	MEG_3747	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTB	NA
contig00020	7435	10512	MDTC	0/0	100.0	99.9	MEG_3749	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTC	NA
contig00028	29873	31030	MDTE	0/0	100.0	100.0	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00028	26735	29848	MDTF	0/0	100.0	100.0	MEG_3752	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTF	NA
contig00008	82627	83853	MDTG	0/0	100.0	100.0	MEG_3753	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig00008	72791	73999	MDTH	0/0	100.0	99.8	MEG_3755	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTH	NA
contig00014	76122	76451	MDTI	0/0	100.0	100.0	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00014	75770	76135	MDTJ	0/0	100.0	99.5	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00014	4368	5741	MDTK	0/0	100.0	100.0	MEG_3759	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:MDTK	NA
contig00067	263	1474	MDTM	0/0	98.3	95.5	MEG_3761	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTM	NA
contig00043	2261	3292	MDTN	0/0	100.0	100.0	MEG_3763	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN	NA
contig00043	3292	5343	MDTO	0/0	100.0	100.0	MEG_3764	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTO	NA
contig00043	5340	6806	MDTP	0/0	100.0	100.0	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig00161	69	962	MPHA	0/0	98.7	100.0	MEG_4029	Drugs:MLS:Macrolide_phosphotransferases:MPHA	NA
contig00007	9441	9915	MPHB	0/0	99.6	97.3	MEG_4033	Drugs:MLS:Macrolide_phosphotransferases:MPHB	NA
contig00016	51586	53334	MSBA	0/0	100.0	100.0	MEG_4061	Drugs:Multi-drug_resistance:Multi-drug_ABC_efflux_pumps:MSBA	NA
contig00021	14767	16668	PBP2	0/0	100.0	100.0	MEG_5400	Drugs:betalactams:Penicillin_binding_protein:PBP2	NA
contig00002	148304	149608	PBP4B	0/0	100.0	100.0	MEG_5409	Drugs:betalactams:Penicillin_binding_protein:PBP4B	NA
contig00004	14362	15330	PMRF	0/0	100.0	99.4	MEG_5801	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF	NA
contig00048	21743	22612	ROBA	0/0	100.0	99.1	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00043	28874	29196	SOXS	0/0	99.7	99.7	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00096	2704	3671	SULI	0/0	100.0	100.0	MEG_6615	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULI	NA
contig00109	85	900	SULII	0/0	100.0	100.0	MEG_6617	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULII	NA
contig00115	1570	2775	TETB	0/0	100.0	100.0	MEG_7052	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETB	NA
contig00115	3569	3985	TETD	0/0	100.0	100.0	MEG_7070	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETD	NA
contig00004	62509	64152	YOGI	0/0	100.0	98.1	MEG_7842	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:YOGI	NA

ID034I

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00053	6749	7552	aph(3’’)-Ib_5	0/0	100.0	99.9	AF321551	aph(3’’)-Ib	Streptomycin
contig00053	5913	6749	aph(6)-Id_1	0/0	100.0	99.9	M28829	aph(6)-Id	Streptomycin
contig00053	429	1304	blaCTX-M-27_1	0/0	100.0	100.0	AY156923	blaCTX-M-27	Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig00053	4822	5682	blaTEM-1B_1	0/0	100.0	100.0	AY458016	blaTEM-1B	Amoxicillin, Ampicillin, Cephalothin, Piperacillin, Ticarcillin
contig00076	90	731	catA2_1	0/0	100.0	96.1	X53796	catA2	Chloramphenicol
contig00087	6	488	dfrA14_5	0/0	100.0	99.6	DQ388123	dfrA14	Trimethoprim
contig00071	265	1028	erm(B)_18	2/2	100.0	99.0	X66468	erm(B)	Erythromycin, Lincomycin, Clindamycin, Quinupristin, Pristinamycin_IA, Virginiamycin_S
contig00004	148578	149810	mdf(A)_1	0/0	100.0	99.8	Y08743	mdf(A)
contig00081	68	943	mph(A)_1	0/0	96.7	100.0	D16251	mph(A)	Erythromycin, Azithromycin, Spiramycin, Telithromycin
contig00053	7613	8428	sul2_2	0/0	100.0	100.0	AY034138	sul2	Sulfamethoxazole
contig00065	1712	2958	tet(A)_6	0/0	97.8	100.0	AF534183	tet(A)	Doxycycline, Tetracycline

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00003	39346	42495	acrB	0/0	100.0	100.0	U00096.3:484403-481253	Protein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug/proton antiporter.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00012	83901	87014	acrD	0/0	100.0	100.0	AP009048.1:2586250-2589364	AcrD is an aminoglycoside efflux pump expressed in E. coli. Its expression can be induced by indole and is regulated by baeRS and cpxAR.	aminoglycoside
contig00049	20439	21060	acrS	0/0	93.8	99.7	U00096:3413465-3412802	AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.	cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00053	6749	7552	APH(3’’)-Ib	0/0	100.0	99.6	AF313472:15593-16397	APH(3’’)-Ib is an aminoglycoside phosphotransferase encoded by plasmids transposons integrative conjugative elements and chromosomes in Enterobacteriaceae and Pseudomonas spp.	aminoglycoside
contig00053	5913	6749	APH(6)-Id	0/0	100.0	99.8	AF024602:3155-3992	APH(6)-Id is an aminoglycoside phosphotransferase encoded by plasmids integrative conjugative elements and chromosomal genomic islands in K. pneumoniae Salmonella spp. E. coli Shigella flexneri Providencia alcalifaciens Pseudomonas spp. V. cholerae Edwardsiella tarda Pasteurella multocida and Aeromonas bestiarum	aminoglycoside
contig00009	67807	68628	bacA	0/0	100.0	100.0	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00018	45780	46502	baeR	0/0	100.0	100.0	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00018	44380	45783	baeS	0/0	100.0	100.0	AP009048:2165012-2166416	BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.	aminocoumarin, aminoglycoside
contig00076	90	731	catII_from_Escherichia_coli_K-12	0/0	100.0	96.1	X53796.1:186-828	catII is a chloramphenicol acetyltransferase. This particular catII is found in E.coli K-12. Confers resistance to chloramphenicol.	phenicol
contig00013	61323	62696	cpxA	0/0	100.0	99.0	BA000007.3:4905062-4903688	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	aminocoumarin, aminoglycoside
contig00010	15377	16009	CRP	0/0	100.0	99.7	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00053	429	1304	CTX-M-27	0/0	100.0	100.0	AY156923:0-876	CTX-M-27 is a beta-lactamase found in Escherichia coli	cephalosporin
contig00087	6	488	dfrA14	0/0	100.0	99.8	EU780012:2162-2645	dfrA14 is an integron-encoded dihydrofolate reductase found in Escherichia coli	diaminopyrimidine
contig00002	58647	59819	emrA	0/0	100.0	100.0	AP009048:2810082-2811255	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	fluoroquinolone
contig00002	59836	61374	emrB	0/0	100.0	100.0	U00096:2812615-2814154	emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin.	fluoroquinolone
contig00014	66331	67386	emrK	0/0	100.0	99.9	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00002	57990	58520	emrR	0/0	100.0	99.8	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00014	64793	66331	emrY	0/0	100.0	99.9	D78168:1591-3130	emrY is a multidrug transport that moves substrates across the inner membrane of the Gram-negative E. coli. It is a homolog of emrB.	tetracycline
contig00005	120315	121958	eptA	0/0	100.0	99.9	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00071	291	1036	ErmB	1/1	99.9	99.2	AF242872.1:2131-2878	ErmB confers the MLSb phenotype. Similar to ErmC expression of ErmB is inducible by erythromycin. The leader peptide causes attenuation of the mRNA and stabilizes the structure preventing further translation. When erythromycin is present it binds the leader peptide causing a change in conformation allowing for the expression of ErmB.	lincosamide, macrolide, streptogramin
contig00003	38130	39323	Escherichia_coli_acrA	0/0	100.0	100.0	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00005	164180	165313	Escherichia_coli_ampC	0/0	100.0	100.0	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00012	118413	119717	Escherichia_coli_ampC1_beta-lactamase	0/0	100.0	100.0	FN649414.1:2765050-2766355	An ampC-like beta-lactamase identified from Escherichia coli.	cephalosporin, penam
contig00003	127462	128619	Escherichia_coli_ampH	0/0	100.0	100.0	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig00004	148578	149810	Escherichia_coli_mdfA	0/0	100.0	98.4	JQ394987:0-1233	Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter.	benzalkonium_chloride, rhodamine, tetracycline
contig00014	67910	68524	evgA	0/0	100.0	100.0	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00014	68529	72122	evgS	0/0	100.0	100.0	U00096:2484373-2487967	EvgS is a sensor protein that phosphorylates the regulatory protein EvgA. evgS corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	fluoroquinolone, macrolide, penam, tetracycline
contig00033	2384	3112	gadW	0/0	100.0	94.7	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig00033	1192	2016	gadX	0/0	100.0	100.0	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00030	5286	5699	H-NS	0/0	100.0	99.3	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00016	8068	8745	kdpE	0/0	100.0	100.0	U00096.3:721733-721055	kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding.	aminoglycoside
contig00027	47772	48155	marA	0/0	100.0	100.0	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00018	35520	36767	mdtA	0/0	100.0	97.9	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00018	36767	39889	mdtB	0/0	100.0	97.6	U00096:2155262-2158385	MdtB is a transporter that forms a heteromultimer complex with MdtC to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex.	aminocoumarin
contig00018	39890	42967	mdtC	0/0	100.0	98.4	U00096:2158385-2161463	MdtC is a transporter that forms a heteromultimer complex with MdtB to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex. In the absence of MdtB MdtC can form a homomultimer complex that results in a functioning efflux complex with a narrower drug specificity. mdtC corresponds to 3 loci in Pseudomonas aeruginosa PAO1 (gene name: muxC/muxB) and 3 loci in Pseudomonas aeruginosa LESB58.	aminocoumarin
contig00033	6613	7770	mdtE	0/0	100.0	100.0	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00033	3475	6588	mdtF	0/0	100.0	100.0	U00096:3660413-3663527	MdtF is the multidrug inner membrane transporter for the MdtEF-TolC efflux complex.	fluoroquinolone, macrolide, penam
contig00007	18580	19806	mdtG	0/0	100.0	99.4	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00007	28435	29643	mdtH	0/0	100.0	99.9	U00096:1125326-1124117	Multidrug resistance protein MdtH	fluoroquinolone
contig00038	9814	11025	mdtM	0/0	98.3	95.5	U00096.3:4568519-4567286	Multidrug resistance protein MdtM	acridine_dye, fluoroquinolone, lincosamide, nucleoside, phenicol
contig00005	89446	90477	mdtN	0/0	100.0	100.0	AP009048.1:4307588-4306556	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	acridine_dye, nucleoside
contig00005	87395	89446	mdtO	0/0	100.0	100.0	AP009048.1:4306557-4304505	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00005	85932	87398	mdtP	0/0	100.0	100.0	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00081	68	943	mphA	0/0	96.7	100.0	D16251.1:2531-1625	The mphA gene encodes for resistance enzyme MPH(2’)-I which preferentially inactivate 14-membered macrolides (e.g.erythromycin telithromycin roxithromycin) over 16-membered macrolides (e.g.tylosin spiramycin). It phosphorylates macrolides at 2’-OH hydroxyl of desosamine sugar of macrolides in a GTP-dependent manner.	macrolide
contig00012	62739	63215	mphB	0/0	100.0	98.3	AE005174.2:3397370-3397847	The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides.	macrolide
contig00006	51374	53122	msbA	0/0	100.0	100.0	U00096.3:966620-968369	MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability.	nitroimidazole
contig00021	62202	63170	pmrF	0/0	100.0	100.0	U00096:2367070-2368039	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide
contig00053	7613	8428	sul2	0/0	100.0	100.0	AY055428.1:21084-20268	Sul2 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria usually found on small plasmids.	sulfonamide
contig00053	4822	5682	TEM-1	0/0	100.0	99.9	AL513383:161910-162771	TEM-1 is a broad-spectrum beta-lactamase found in many Gram-negative bacteria. Confers resistance to penicillins and first generation cephalosphorins.	cephalosporin, monobactam, penam, penem
contig00065	1712	2958	tet(A)	0/0	97.8	100.0	AF534183.1:2970-4245	TetA is a tetracycline efflux pump found in many species of Gram-negative bacteria.	tetracycline
contig00009	43942	45429	tolC	0/0	100.0	100.0	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan
contig00021	2099	3742	yojI	0/0	100.0	100.0	U00096.3:2308615-2306971	YojI mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. YojI is capable of pumping out microcin molecules. The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI.	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00053	6749	7552	(AGly)strA	0/0	100.0	99.8	AB366441:22458-23261	(AGly)strA	NA
contig00053	5913	6749	(AGly)strB	0/0	100.0	99.9	FJ474091:264-1100	(AGly)strB	NA
contig00012	118413	119717	(Bla)AmpC1_Ecoli	0/0	100.0	100.0	FN649414:2765051-2766355	(Bla)AmpC1_Ecoli	NA
contig00005	164180	165313	(Bla)AmpC2_Ecoli	0/0	100.0	100.0	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00003	127462	128619	(Bla)ampH_Ecoli	0/0	100.0	100.0	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00053	429	1304	(Bla)blaCTX-M-27	0/0	100.0	100.0	AY156923:1-876	(Bla)blaCTX-M-27	NA
contig00053	4822	5682	(Bla)blaTEM-105	0/0	100.0	99.9	AF516720:215-1075	(Bla)blaTEM-105	NA
contig00016	60156	62057	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100.0	100.0	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA
contig00071	291	1028	(MLS)erm(B)	0/0	100.0	99.6	M11180:714-1451	(MLS)erm(B)	NA
contig00081	68	943	(MLS)mph(A)	0/0	96.7	100.0	DQ445270:1626-2531	(MLS)mph(A)	NA
contig00076	90	731	(Phe)catA2	0/0	100.0	96.1	X53796:187-903	(Phe)catA2	NA
contig00053	7613	8428	(Sul)sul2	0/0	100.0	100.0	EU360945:1617-2432	(Sul)sul2	NA
contig00065	1684	2958	(Tet)tetA	0/0	100.0	100.0	JX424423:94438-95712	(Tet)tetA	NA
contig00087	6	479	(Tmt)dfrA14	0/0	100.0	100.0	GU726917:72-545	(Tmt)dfrA14	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00053	6749	7576	aph(3’’)-Ib	0/0	100.0	99.9	NG_056002.2	aminoglycoside O-phosphotransferase APH(3’’)-Ib	STREPTOMYCIN
contig00053	5913	6749	aph(6)-Id	0/0	100.0	100.0	NG_047466.1	aminoglycoside O-phosphotransferase APH(6)-Id	STREPTOMYCIN
contig00053	429	1304	blaCTX-M-27	0/0	100.0	100.0	NG_048976.1	class A extended-spectrum beta-lactamase CTX-M-27	CEPHALOSPORIN
contig00005	164180	165313	blaEC	0/0	100.0	100.0	NG_047494.1	BlaEC family class C beta-lactamase	BETA-LACTAM
contig00053	4822	5682	blaTEM-1	0/0	100.0	100.0	NG_050145.1	class A broad-spectrum beta-lactamase TEM-1	BETA-LACTAM
contig00076	90	731	catA2	0/0	100.0	100.0	NG_047596.1	type A-2 chloramphenicol O-acetyltransferase CatII	CHLORAMPHENICOL
contig00087	6	479	dfrA14	0/0	100.0	100.0	NG_056035.1	trimethoprim-resistant dihydrofolate reductase DfrA14	TRIMETHOPRIM
contig00071	291	1028	erm(B)	0/0	100.0	99.9	NG_047804.1	23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(B)	MACROLIDE
contig00081	68	943	mph(A)	0/0	96.7	100.0	NG_047985.1	Mph(A) family macrolide 2’-phosphotransferase	MACROLIDE
contig00053	7613	8428	sul2	0/0	100.0	100.0	NG_051852.1	sulfonamide-resistant dihydropteroate synthase Sul2	SULFONAMIDE
contig00065	1684	2883	tet(A)	0/0	100.0	100.0	NG_048154.1	tetracycline efflux MFS transporter Tet(A)	TETRACYCLINE

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00003	38130	39323	ACRA	0/0	100.0	100.0	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00003	39346	42495	ACRB	0/0	100.0	100.0	MEG_401	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRB	NA
contig00012	83901	87014	ACRD	0/0	100.0	100.0	MEG_407	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ACRD	NA
contig00049	20439	21060	ACRS	0/0	93.8	99.7	MEG_415	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS	NA
contig00005	164180	165313	AMPC	0/0	100.0	100.0	MEG_728	Drugs:betalactams:Class_C_betalactamases:AMPC	NA
contig00003	127462	128619	AMPH	0/0	100.0	100.0	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00053	6749	7576	APH3-DPRIME	0/0	100.0	99.9	MEG_1019	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH3-DPRIME	NA
contig00053	5913	6749	APH6	0/0	100.0	100.0	MEG_1084	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH6	NA
contig00018	21255	23107	ASMA	0/0	100.0	96.9	MEG_1180	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:ASMA	NA
contig00009	67807	68628	BACA	0/0	100.0	100.0	MEG_1190	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00018	45780	46502	BAER	0/0	100.0	100.0	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00018	44380	45783	BAES	0/0	100.0	100.0	MEG_1193	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES	NA
contig00024	49248	50438	BCR	0/0	100.0	99.9	MEG_1210	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR	NA
contig00076	90	731	CATA	0/0	100.0	100.0	MEG_1568	Drugs:Phenicol:Chloramphenicol_acetyltransferases:CATA	NA
contig00013	60628	61326	CPXAR	0/0	100.0	100.0	MEG_2122	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00013	61323	62696	CPXAR	0/0	100.0	100.0	MEG_2121	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00010	15377	16009	CRP	0/0	100.0	99.7	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00053	407	1310	CTX	0/0	100.0	99.8	MEG_2401	Drugs:betalactams:Class_A_betalactamases:CTX	NA
contig00053	1339	2281	CTX	0/0	100.0	100.0	MEG_2435	Drugs:betalactams:Class_A_betalactamases:CTX	NA
contig00087	6	479	DFRA	0/0	100.0	99.8	MEG_2517	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00002	58647	59819	EMRA	0/0	100.0	100.0	MEG_2722	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA	NA
contig00002	59836	61374	EMRB	0/0	100.0	100.0	MEG_2725	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRB	NA
contig00015	75505	76695	EMRD	0/0	100.0	100.0	MEG_2729	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD	NA
contig00014	66331	67494	EMRK	0/0	100.0	99.9	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig00002	57990	58520	EMRR	0/0	100.0	99.8	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00014	64793	66331	EMRY	0/0	100.0	99.9	MEG_2736	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRY	NA
contig00005	120315	121958	EPTA	0/0	100.0	99.9	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig00071	265	1028	ERMB	2/2	100.0	99.0	MEG_2801	Drugs:MLS:23S_rRNA_methyltransferases:ERMB	NA
contig00014	68529	72122	EVGS	0/0	100.0	100.0	MEG_2870	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EVGS	NA
contig00033	2384	3112	GADW	0/0	100.0	100.0	MEG_3081	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig00033	1192	2016	GADX	0/0	100.0	100.0	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00030	5286	5699	HNS	0/0	100.0	99.3	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00016	8068	8745	KDPE	0/0	100.0	100.0	MEG_3448	Drugs:Aminoglycosides:Aminoglycoside_efflux_pumps:KDPE	NA
contig00027	47766	48155	MARA	0/0	100.0	100.0	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00027	47318	47752	MARR	0/0	100.0	100.0	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00004	148578	149810	MDFA	0/0	100.0	99.9	MEG_3737	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDFA	NA
contig00018	35520	36767	MDTA	0/0	100.0	97.9	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00018	36767	39889	MDTB	0/0	100.0	97.6	MEG_3747	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTB	NA
contig00018	39890	42967	MDTC	0/0	100.0	98.4	MEG_3749	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTC	NA
contig00033	6613	7770	MDTE	0/0	100.0	100.0	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00033	3475	6588	MDTF	0/0	100.0	100.0	MEG_3752	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTF	NA
contig00007	18580	19806	MDTG	0/0	100.0	100.0	MEG_3753	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig00007	28435	29643	MDTH	0/0	100.0	99.9	MEG_3755	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTH	NA
contig00001	427030	427359	MDTI	0/0	100.0	100.0	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00001	426678	427043	MDTJ	0/0	100.0	99.5	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00001	355276	356649	MDTK	0/0	100.0	100.0	MEG_3759	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:MDTK	NA
contig00038	9814	11025	MDTM	0/0	98.3	95.5	MEG_3761	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTM	NA
contig00005	89446	90477	MDTN	0/0	100.0	100.0	MEG_3763	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN	NA
contig00005	87395	89446	MDTO	0/0	100.0	100.0	MEG_3764	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTO	NA
contig00005	85932	87398	MDTP	0/0	100.0	100.0	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig00081	68	943	MPHA	0/0	96.7	100.0	MEG_4029	Drugs:MLS:Macrolide_phosphotransferases:MPHA	NA
contig00012	62739	63215	MPHB	0/0	100.0	98.3	MEG_4033	Drugs:MLS:Macrolide_phosphotransferases:MPHB	NA
contig00006	51374	53122	MSBA	0/0	100.0	100.0	MEG_4061	Drugs:Multi-drug_resistance:Multi-drug_ABC_efflux_pumps:MSBA	NA
contig00016	60156	62057	PBP2	0/0	100.0	100.0	MEG_5400	Drugs:betalactams:Penicillin_binding_protein:PBP2	NA
contig00012	118413	119717	PBP4B	0/0	100.0	100.0	MEG_5409	Drugs:betalactams:Penicillin_binding_protein:PBP4B	NA
contig00021	62202	63170	PMRF	0/0	100.0	100.0	MEG_5801	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF	NA
contig00032	4214	5083	ROBA	0/0	100.0	99.0	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00005	63992	64315	SOXS	0/0	100.0	100.0	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00053	7613	8428	SULII	0/0	100.0	100.0	MEG_6617	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULII	NA
contig00053	4455	5700	TEM	0/0	98.3	99.4	MEG_6875	Drugs:betalactams:Class_A_betalactamases:TEM	NA
contig00065	1684	2958	TETA	0/0	100.0	100.0	MEG_7024	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETA	NA
contig00021	2099	3742	YOGI	0/0	100.0	100.0	MEG_7842	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:YOGI	NA

ID041

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00045	23105	23908	aph(3’’)-Ib_5	0/0	100.0	100.0	AF321551	aph(3’’)-Ib	Streptomycin
contig00045	22269	23105	aph(6)-Id_1	0/0	100.0	100.0	M28829	aph(6)-Id	Streptomycin
contig00045	16991	17866	blaCTX-M-15_1	0/0	100.0	100.0	AY044436	blaCTX-M-15	Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig00045	20688	21548	blaTEM-1B_1	0/0	100.0	100.0	AY458016	blaTEM-1B	Amoxicillin, Ampicillin, Cephalothin, Piperacillin, Ticarcillin
contig00078	182	664	dfrA14_5	0/0	100.0	99.6	DQ388123	dfrA14	Trimethoprim
contig00018	32387	33619	mdf(A)_1	0/0	100.0	97.7	Y08743	mdf(A)
contig00045	11694	12350	qnrS1_1	0/0	100.0	100.0	AB187515	qnrS1	Ciprofloxacin
contig00045	23969	24784	sul2_2	0/0	100.0	100.0	AY034138	sul2	Sulfamethoxazole
contig00063	4861	6107	tet(A)_6	0/0	97.8	100.0	AF534183	tet(A)	Doxycycline, Tetracycline

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00013	51650	54799	acrB	0/0	100.0	99.1	U00096.3:484403-481253	Protein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug/proton antiporter.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00006	136643	139756	acrD	0/0	100.0	98.8	AP009048.1:2586250-2589364	AcrD is an aminoglycoside efflux pump expressed in E. coli. Its expression can be induced by indole and is regulated by baeRS and cpxAR.	aminoglycoside
contig00034	8641	9798	acrE	0/0	100.0	97.8	U00096:3413863-3415021	AcrE is a membrane fusion protein similar to AcrA.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00034	5525	8629	acrF	0/0	100.0	97.5	U00096:3415032-3418137	AcrF is a inner membrane transporter similar to AcrB.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00034	10197	10859	acrS	0/0	100.0	97.6	U00096:3413465-3412802	AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.	cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00045	23105	23908	APH(3’’)-Ib	0/0	100.0	99.8	AF313472:15593-16397	APH(3’’)-Ib is an aminoglycoside phosphotransferase encoded by plasmids transposons integrative conjugative elements and chromosomes in Enterobacteriaceae and Pseudomonas spp.	aminoglycoside
contig00045	22269	23105	APH(6)-Id	0/0	100.0	99.9	AF024602:3155-3992	APH(6)-Id is an aminoglycoside phosphotransferase encoded by plasmids integrative conjugative elements and chromosomal genomic islands in K. pneumoniae Salmonella spp. E. coli Shigella flexneri Providencia alcalifaciens Pseudomonas spp. V. cholerae Edwardsiella tarda Pasteurella multocida and Aeromonas bestiarum	aminoglycoside
contig00005	42403	43222	bacA	0/0	99.8	97.3	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00020	10764	11485	baeR	0/0	99.9	96.7	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00020	9364	10767	baeS	0/0	100.0	97.3	AP009048:2165012-2166416	BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.	aminocoumarin, aminoglycoside
contig00026	10948	12321	cpxA	0/0	100.0	98.5	BA000007.3:4905062-4903688	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	aminocoumarin, aminoglycoside
contig00016	15385	16017	CRP	0/0	100.0	98.7	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00045	16991	17866	CTX-M-15	0/0	100.0	100.0	AY044436:1435-2311	CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family	cephalosporin
contig00078	182	664	dfrA14	0/0	100.0	99.8	EU780012:2162-2645	dfrA14 is an integron-encoded dihydrofolate reductase found in Escherichia coli	diaminopyrimidine
contig00001	391363	392535	emrA	0/0	100.0	98.1	AP009048:2810082-2811255	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	fluoroquinolone
contig00001	389808	391346	emrB	0/0	100.0	98.0	U00096:2812615-2814154	emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin.	fluoroquinolone
contig00021	58475	59530	emrK	0/0	100.0	97.6	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00001	392662	393192	emrR	0/0	100.0	99.4	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00021	56937	58475	emrY	0/0	100.0	97.7	D78168:1591-3130	emrY is a multidrug transport that moves substrates across the inner membrane of the Gram-negative E. coli. It is a homolog of emrB.	tetracycline
contig00015	92678	94321	eptA	0/0	100.0	98.0	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00013	54822	56015	Escherichia_coli_acrA	0/0	100.0	98.9	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00015	49626	50759	Escherichia_coli_ampC	0/0	100.0	98.0	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00006	170878	172182	Escherichia_coli_ampC1_beta-lactamase	0/0	100.0	95.9	FN649414.1:2765050-2766355	An ampC-like beta-lactamase identified from Escherichia coli.	cephalosporin, penam
contig00008	14998	16155	Escherichia_coli_ampH	0/0	100.0	98.3	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig00018	32387	33619	Escherichia_coli_mdfA	0/0	100.0	96.2	JQ394987:0-1233	Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter.	benzalkonium_chloride, rhodamine, tetracycline
contig00021	60054	60668	evgA	0/0	100.0	99.2	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00021	60673	64266	evgS	0/0	100.0	96.9	U00096:2484373-2487967	EvgS is a sensor protein that phosphorylates the regulatory protein EvgA. evgS corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	fluoroquinolone, macrolide, penam, tetracycline
contig00014	44014	44742	gadW	0/0	100.0	94.9	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig00014	42821	43645	gadX	0/0	100.0	97.1	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00027	1490	1903	H-NS	0/0	100.0	99.5	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00011	8204	8879	kdpE	0/0	99.7	95.7	U00096.3:721733-721055	kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding.	aminoglycoside
contig00009	101666	102049	marA	0/0	100.0	99.5	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00020	504	1751	mdtA	0/0	100.0	96.9	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00020	1751	4873	mdtB	0/0	100.0	96.8	U00096:2155262-2158385	MdtB is a transporter that forms a heteromultimer complex with MdtC to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex.	aminocoumarin
contig00020	4874	7951	mdtC	0/0	100.0	96.7	U00096:2158385-2161463	MdtC is a transporter that forms a heteromultimer complex with MdtB to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex. In the absence of MdtB MdtC can form a homomultimer complex that results in a functioning efflux complex with a narrower drug specificity. mdtC corresponds to 3 loci in Pseudomonas aeruginosa PAO1 (gene name: muxC/muxB) and 3 loci in Pseudomonas aeruginosa LESB58.	aminocoumarin
contig00014	48243	49400	mdtE	0/0	100.0	98.7	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00014	45105	48218	mdtF	0/0	100.0	98.7	U00096:3660413-3663527	MdtF is the multidrug inner membrane transporter for the MdtEF-TolC efflux complex.	fluoroquinolone, macrolide, penam
contig00012	112413	113639	mdtG	0/0	100.0	98.2	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00012	102574	103782	mdtH	0/0	100.0	97.8	U00096:1125326-1124117	Multidrug resistance protein MdtH	fluoroquinolone
contig00010	89216	90448	mdtM	0/0	100.0	96.9	U00096.3:4568519-4567286	Multidrug resistance protein MdtM	acridine_dye, fluoroquinolone, lincosamide, nucleoside, phenicol
contig00019	2612	3643	mdtN	0/0	100.0	97.6	AP009048.1:4307588-4306556	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	acridine_dye, nucleoside
contig00019	3643	5694	mdtO	0/0	100.0	96.8	AP009048.1:4306557-4304505	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00019	5691	7157	mdtP	0/0	100.0	97.0	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00006	115462	115936	mphB	0/0	99.6	96.6	AE005174.2:3397370-3397847	The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides.	macrolide
contig00023	6476	8224	msbA	0/0	100.0	99.1	U00096.3:966620-968369	MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability.	nitroimidazole
contig00007	173975	174943	pmrF	0/0	100.0	98.8	U00096:2367070-2368039	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide
contig00045	11694	12350	QnrS1	0/0	100.0	100.0	DQ485529.1:0-657	QnrS1 is a plasmid-mediated quinolone resistance protein found in Shigella flexneri	fluoroquinolone
contig00045	23969	24784	sul2	0/0	100.0	100.0	AY055428.1:21084-20268	Sul2 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria usually found on small plasmids.	sulfonamide
contig00045	20688	21548	TEM-1	0/0	100.0	99.9	AL513383:161910-162771	TEM-1 is a broad-spectrum beta-lactamase found in many Gram-negative bacteria. Confers resistance to penicillins and first generation cephalosphorins.	cephalosporin, monobactam, penam, penem
contig00063	4861	6107	tet(A)	0/0	97.8	100.0	AF534183.1:2970-4245	TetA is a tetracycline efflux pump found in many species of Gram-negative bacteria.	tetracycline
contig00005	18889	20376	tolC	0/0	100.0	97.9	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan
contig00007	112256	113899	yojI	0/0	100.0	98.3	U00096.3:2308615-2306971	YojI mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. YojI is capable of pumping out microcin molecules. The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI.	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00045	23105	23908	(AGly)strA	0/0	100	99.9	AB366441:22458-23261	(AGly)strA	NA
contig00045	22269	23105	(AGly)strB	0/0	100	100.0	FJ474091:264-1100	(AGly)strB	NA
contig00006	170878	172182	(Bla)AmpC1_Ecoli	0/0	100	95.9	FN649414:2765051-2766355	(Bla)AmpC1_Ecoli	NA
contig00015	49626	50759	(Bla)AmpC2_Ecoli	0/0	100	98.0	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00008	14998	16155	(Bla)ampH_Ecoli	0/0	100	98.3	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00045	16991	17866	(Bla)blaCTX-M-15	0/0	100	100.0	JQ686199:261-1136	(Bla)blaCTX-M-15	NA
contig00045	20688	21548	(Bla)blaTEM-105	0/0	100	99.9	AF516720:215-1075	(Bla)blaTEM-105	NA
contig00011	47276	49177	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100	98.7	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA
contig00045	11694	12350	(Flq)qnr-S1	0/0	100	100.0	AB187515:9737-10393	(Flq)qnr-S1	NA
contig00045	23969	24784	(Sul)sul2	0/0	100	100.0	EU360945:1617-2432	(Sul)sul2	NA
contig00063	4833	6107	(Tet)tetA	0/0	100	100.0	JX424423:94438-95712	(Tet)tetA	NA
contig00078	182	655	(Tmt)dfrA14	0/0	100	100.0	GU726917:72-545	(Tmt)dfrA14	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00045	23105	23932	aph(3’’)-Ib	0/0	100	100.0	NG_056002.2	aminoglycoside O-phosphotransferase APH(3’’)-Ib	STREPTOMYCIN
contig00045	22269	23105	aph(6)-Id	0/0	100	100.0	NG_047464.1	aminoglycoside O-phosphotransferase APH(6)-Id	STREPTOMYCIN
contig00045	16991	17866	blaCTX-M-15	0/0	100	100.0	NG_048935.1	class A extended-spectrum beta-lactamase CTX-M-15	CEPHALOSPORIN
contig00015	49626	50759	blaEC-8	0/0	100	98.2	NG_049086.1	cephalosporin-hydrolyzing class C beta-lactamase EC-8	CEPHALOSPORIN
contig00045	20688	21548	blaTEM-1	0/0	100	100.0	NG_050145.1	class A broad-spectrum beta-lactamase TEM-1	BETA-LACTAM
contig00078	182	655	dfrA14	0/0	100	100.0	NG_056035.1	trimethoprim-resistant dihydrofolate reductase DfrA14	TRIMETHOPRIM
contig00045	11694	12350	qnrS1	0/0	100	100.0	NG_050543.1	quinolone resistance pentapeptide repeat protein QnrS1	QUINOLONE
contig00045	23969	24784	sul2	0/0	100	100.0	NG_051852.1	sulfonamide-resistant dihydropteroate synthase Sul2	SULFONAMIDE
contig00063	4833	6032	tet(A)	0/0	100	100.0	NG_048154.1	tetracycline efflux MFS transporter Tet(A)	TETRACYCLINE

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00013	54822	56015	ACRA	0/0	100.0	98.9	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00013	51650	54799	ACRB	0/0	100.0	99.1	MEG_401	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRB	NA
contig00006	136643	139756	ACRD	0/0	100.0	98.8	MEG_407	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ACRD	NA
contig00034	8641	9798	ACRE	0/0	100.0	97.8	MEG_408	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRE	NA
contig00034	5525	8629	ACRF	0/0	100.0	97.5	MEG_409	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRF	NA
contig00034	10197	10859	ACRS	0/0	100.0	97.6	MEG_415	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS	NA
contig00008	14998	16155	AMPH	0/0	100.0	98.3	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00045	23105	23932	APH3-DPRIME	0/0	100.0	100.0	MEG_1019	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH3-DPRIME	NA
contig00045	22269	23105	APH6	0/0	100.0	100.0	MEG_1086	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH6	NA
contig00017	95171	97023	ASMA	0/0	100.0	97.5	MEG_1180	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:ASMA	NA
contig00005	42403	43222	BACA	0/0	99.8	97.8	MEG_1189	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00020	10764	11485	BAER	0/0	99.9	96.7	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00020	9364	10767	BAES	0/0	100.0	97.3	MEG_1193	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES	NA
contig00007	85796	86986	BCR	0/0	100.0	96.3	MEG_1210	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR	NA
contig00015	49626	50759	BLAEC	0/0	100.0	98.2	MEG_1278	Drugs:betalactams:Class_C_betalactamases:BLAEC	NA
contig00026	10948	12321	CPXAR	0/0	100.0	98.5	MEG_2119	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00026	12318	13016	CPXAR	0/0	100.0	99.7	MEG_2122	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00016	15385	16017	CRP	0/0	100.0	98.7	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00078	182	655	DFRA	0/0	100.0	99.8	MEG_2517	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00001	391363	392535	EMRA	0/0	100.0	98.1	MEG_2722	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA	NA
contig00001	389808	391346	EMRB	0/0	100.0	98.0	MEG_2725	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRB	NA
contig00003	138194	139384	EMRD	0/0	100.0	97.9	MEG_2729	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD	NA
contig00021	58475	59638	EMRK	0/0	100.0	97.8	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig00001	392662	393192	EMRR	0/0	100.0	99.4	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00021	56937	58475	EMRY	0/0	100.0	97.7	MEG_2736	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRY	NA
contig00015	92678	94321	EPTA	0/0	100.0	98.0	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig00021	60673	64266	EVGS	0/0	100.0	97.5	MEG_2869	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EVGS	NA
contig00014	44014	44742	GADW	0/0	100.0	97.7	MEG_3081	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig00014	42821	43645	GADX	0/0	100.0	97.1	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00027	1490	1903	HNS	0/0	100.0	99.5	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00011	8204	8879	KDPE	0/0	99.7	95.7	MEG_3448	Drugs:Aminoglycosides:Aminoglycoside_efflux_pumps:KDPE	NA
contig00009	101660	102049	MARA	0/0	100.0	99.5	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00009	101211	101645	MARR	0/0	100.0	97.9	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00018	32387	33619	MDFA	0/0	100.0	97.8	MEG_3737	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDFA	NA
contig00020	504	1751	MDTA	0/0	100.0	96.9	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00020	1751	4873	MDTB	0/0	100.0	96.8	MEG_3747	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTB	NA
contig00020	4874	7951	MDTC	0/0	100.0	96.7	MEG_3749	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTC	NA
contig00014	48243	49400	MDTE	0/0	100.0	98.7	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00014	45105	48218	MDTF	0/0	100.0	98.7	MEG_3752	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTF	NA
contig00012	112413	113639	MDTG	0/0	100.0	98.8	MEG_3753	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig00012	102574	103782	MDTH	0/0	100.0	97.8	MEG_3755	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTH	NA
contig00009	140220	140549	MDTI	0/0	100.0	99.4	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00009	140536	140901	MDTJ	0/0	100.0	100.0	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00002	312556	313928	MDTK	0/0	99.9	98.3	MEG_3759	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:MDTK	NA
contig00010	89216	90448	MDTM	0/0	100.0	96.9	MEG_3761	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTM	NA
contig00019	2612	3643	MDTN	0/0	100.0	97.6	MEG_3763	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN	NA
contig00019	3643	5694	MDTO	0/0	100.0	96.8	MEG_3764	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTO	NA
contig00019	5691	7157	MDTP	0/0	100.0	97.0	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig00006	115462	115936	MPHB	0/0	99.6	96.6	MEG_4033	Drugs:MLS:Macrolide_phosphotransferases:MPHB	NA
contig00023	6476	8224	MSBA	0/0	100.0	99.1	MEG_4061	Drugs:Multi-drug_resistance:Multi-drug_ABC_efflux_pumps:MSBA	NA
contig00011	47276	49177	PBP2	0/0	100.0	98.7	MEG_5400	Drugs:betalactams:Penicillin_binding_protein:PBP2	NA
contig00006	170878	172182	PBP4B	0/0	100.0	95.9	MEG_5409	Drugs:betalactams:Penicillin_binding_protein:PBP4B	NA
contig00007	173975	174943	PMRF	0/0	100.0	98.8	MEG_5801	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF	NA
contig00045	11694	12350	QNRS	0/0	100.0	100.0	MEG_6020	Drugs:Fluoroquinolones:Quinolone_resistance_protein_Qnr:QNRS	NA
contig00010	16140	17009	ROBA	0/0	100.0	99.3	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00019	28801	29123	SOXS	0/0	99.7	98.1	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00045	23969	24784	SULII	0/0	100.0	100.0	MEG_6617	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULII	NA
contig00045	20321	21566	TEM	0/0	98.3	99.4	MEG_6875	Drugs:betalactams:Class_A_betalactamases:TEM	NA
contig00063	4833	6107	TETA	0/0	100.0	100.0	MEG_7024	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETA	NA
contig00007	112256	113899	YOGI	0/0	100.0	98.3	MEG_7842	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:YOGI	NA

ID043I

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00094	33	893	aac(3)-IId_1	0/0	100	99.9	EU022314	aac(3)-IId	Gentamicin, Tobramycin
contig00104	1538	2137	aac(6’)-Ib-cr_1	0/0	100	100.0	DQ303918	aac(6’)-Ib-cr	Ciprofloxacin
contig00076	2472	3260	aadA5_1	0/0	100	100.0	AF137361	aadA5	Streptomycin
contig00082	5399	6178	aph(3’’)-Ib_5	0/0	97	100.0	AF321551	aph(3’’)-Ib	Streptomycin
contig00082	4563	5399	aph(6)-Id_1	0/0	100	100.0	M28829	aph(6)-Id	Streptomycin
contig00085	1871	2746	blaCTX-M-15_1	0/0	100	100.0	AY044436	blaCTX-M-15	Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig00104	577	1407	blaOXA-1_1	0/0	100	100.0	HQ170510	blaOXA-1	Amoxicillin, Amoxicillin+Clavulanic_acid, Ampicillin, Ampicillin+Clavulanic_acid, Cefepime, Piperacillin, Piperacillin+Tazobactam
contig00074	176	1036	blaTEM-1B_1	0/0	100	100.0	AY458016	blaTEM-1B	Amoxicillin, Ampicillin, Cephalothin, Piperacillin, Ticarcillin
contig00084	619	1278	catA1_1	0/0	100	99.8	V00622	catA1	Chloramphenicol
contig00076	1868	2341	dfrA17_1	0/0	100	100.0	FJ460238	dfrA17	Trimethoprim
contig00008	30177	31409	mdf(A)_1	0/0	100	99.9	Y08743	mdf(A)
contig00123	68	989	mph(A)_2	1/1	100	99.7	U36578	mph(A)	Erythromycin, Azithromycin, Spiramycin, Telithromycin
contig00076	3780	4646	sul1_5	0/0	100	99.9	EU780013	sul1	Sulfamethoxazole
contig00082	85	900	sul2_2	0/0	100	100.0	AY034138	sul2	Sulfamethoxazole
contig00088	1998	3203	tet(B)_2	0/0	100	100.0	AF326777	tet(B)	Doxycycline, Tetracycline, Minocycline

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00094	33	893	AAC(3)-IId	0/0	100.0	99.9	EU022314.1:0-861	AAC(3)-IId is a plasmid-encoded aminoglycoside acetyltransferase in E. coli	aminoglycoside
contig00104	1538	2137	AAC(6’)-Ib-cr	0/0	100.0	100.0	DQ303918:0-600	AAC(6’)-Ib-cr is an aminoglycoside acetyltransferase encoded by plasmids transposons integrons in Enterobacteriaceae. The aac(6’)-Ib-cr variant gene can induce resistance against aminoglycoside and fluoroquinolone simultaneously	aminoglycoside, fluoroquinolone
contig00076	2472	3260	aadA5	0/0	100.0	100.0	AF137361:63-852	aadA5 is an aminoglycoside nucleotidyltransferase gene encoded by plasmids transposons and integrons in E. coli K. pneumoniae Kluyvera georgiana P. aeruginosa and E. cloacae	aminoglycoside
contig00002	39346	42495	acrB	0/0	100.0	100.0	U00096.3:484403-481253	Protein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug/proton antiporter.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00006	148083	151196	acrD	0/0	100.0	98.8	AP009048.1:2586250-2589364	AcrD is an aminoglycoside efflux pump expressed in E. coli. Its expression can be induced by indole and is regulated by baeRS and cpxAR.	aminoglycoside
contig00075	5854	8958	acrF	0/0	100.0	100.0	U00096:3415032-3418137	AcrF is a inner membrane transporter similar to AcrB.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00056	20506	21168	acrS	0/0	100.0	100.0	U00096:3413465-3412802	AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.	cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00082	5399	6178	APH(3’’)-Ib	0/0	97.0	99.7	AF313472:15593-16397	APH(3’’)-Ib is an aminoglycoside phosphotransferase encoded by plasmids transposons integrative conjugative elements and chromosomes in Enterobacteriaceae and Pseudomonas spp.	aminoglycoside
contig00082	4563	5399	APH(6)-Id	0/0	100.0	99.9	AF024602:3155-3992	APH(6)-Id is an aminoglycoside phosphotransferase encoded by plasmids integrative conjugative elements and chromosomal genomic islands in K. pneumoniae Salmonella spp. E. coli Shigella flexneri Providencia alcalifaciens Pseudomonas spp. V. cholerae Edwardsiella tarda Pasteurella multocida and Aeromonas bestiarum	aminoglycoside
contig00017	70351	71170	bacA	0/0	99.8	98.5	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00072	10538	11260	baeR	0/0	100.0	99.3	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00072	9138	10541	baeS	0/0	100.0	98.7	AP009048:2165012-2166416	BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.	aminocoumarin, aminoglycoside
contig00084	619	1278	catI	0/0	100.0	99.8	V00622:243-903	catI is a chromosome and transposon-encoded variant of the cat gene found in Escherichia coli and Acinetobacter baumannii	phenicol
contig00013	61576	62949	cpxA	0/0	100.0	99.0	BA000007.3:4905062-4903688	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	aminocoumarin, aminoglycoside
contig00010	15081	15713	CRP	0/0	100.0	99.7	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00085	1871	2746	CTX-M-15	0/0	100.0	100.0	AY044436:1435-2311	CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family	cephalosporin
contig00076	1868	2341	dfrA17	0/0	100.0	100.0	DQ838665:0-474	dfrA17 is an integron-encoded dihydrofolate reductase found in Escherichia coli	diaminopyrimidine
contig00012	47169	48341	emrA	0/0	100.0	97.9	AP009048:2810082-2811255	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	fluoroquinolone
contig00012	48358	49896	emrB	0/0	100.0	98.6	U00096:2812615-2814154	emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin.	fluoroquinolone
contig00001	270703	271758	emrK	0/0	100.0	98.0	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00012	46512	47042	emrR	0/0	100.0	99.4	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00001	269165	270703	emrY	0/0	100.0	97.7	D78168:1591-3130	emrY is a multidrug transport that moves substrates across the inner membrane of the Gram-negative E. coli. It is a homolog of emrB.	tetracycline
contig00018	67027	68670	eptA	0/0	100.0	99.9	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00002	38130	39323	Escherichia_coli_acrA	0/0	100.0	100.0	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00025	38370	39503	Escherichia_coli_ampC	0/0	100.0	97.3	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00001	334197	335495	Escherichia_coli_ampC1_beta-lactamase	0/0	99.5	96.1	FN649414.1:2765050-2766355	An ampC-like beta-lactamase identified from Escherichia coli.	cephalosporin, penam
contig00002	127462	128619	Escherichia_coli_ampH	0/0	100.0	100.0	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig00019	2074	2406	Escherichia_coli_emrE	0/0	100.0	91.9	Z11877.1:485-818	Member of the small MDR (multidrug resistance) family of transporters, in Escherichia coli this protein provides resistance against a number of positively charged compounds including ethidium bromide and erythromycin, proton-dependent secondary transporter which exchanges protons for compound translocation	macrolide
contig00008	30177	31409	Escherichia_coli_mdfA	0/0	100.0	98.4	JQ394987:0-1233	Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter.	benzalkonium_chloride, rhodamine, tetracycline
contig00001	272282	272896	evgA	0/0	100.0	99.2	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00001	272901	276494	evgS	0/0	100.0	96.8	U00096:2484373-2487967	EvgS is a sensor protein that phosphorylates the regulatory protein EvgA. evgS corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	fluoroquinolone, macrolide, penam, tetracycline
contig00037	1784	2512	gadW	0/0	100.0	94.7	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig00037	592	1416	gadX	0/0	100.0	99.9	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00033	5236	5649	H-NS	0/0	100.0	99.3	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00030	8102	8779	kdpE	0/0	100.0	100.0	U00096.3:721733-721055	kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding.	aminoglycoside
contig00004	184592	184975	marA	0/0	100.0	100.0	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00072	278	1525	mdtA	0/0	100.0	98.0	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00072	1525	4647	mdtB	0/0	100.0	97.0	U00096:2155262-2158385	MdtB is a transporter that forms a heteromultimer complex with MdtC to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex.	aminocoumarin
contig00072	4648	7725	mdtC	0/0	100.0	97.7	U00096:2158385-2161463	MdtC is a transporter that forms a heteromultimer complex with MdtB to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex. In the absence of MdtB MdtC can form a homomultimer complex that results in a functioning efflux complex with a narrower drug specificity. mdtC corresponds to 3 loci in Pseudomonas aeruginosa PAO1 (gene name: muxC/muxB) and 3 loci in Pseudomonas aeruginosa LESB58.	aminocoumarin
contig00037	6013	7170	mdtE	0/0	100.0	100.0	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00037	2875	5988	mdtF	0/0	100.0	100.0	U00096:3660413-3663527	MdtF is the multidrug inner membrane transporter for the MdtEF-TolC efflux complex.	fluoroquinolone, macrolide, penam
contig00032	18399	19625	mdtG	0/0	100.0	99.4	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00032	28254	29462	mdtH	0/0	100.0	99.9	U00096:1125326-1124117	Multidrug resistance protein MdtH	fluoroquinolone
contig00044	3939	5171	mdtM	0/0	100.0	100.0	U00096.3:4568519-4567286	Multidrug resistance protein MdtM	acridine_dye, fluoroquinolone, lincosamide, nucleoside, phenicol
contig00048	20339	21370	mdtN	0/0	100.0	100.0	AP009048.1:4307588-4306556	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	acridine_dye, nucleoside
contig00048	18288	20339	mdtO	0/0	100.0	100.0	AP009048.1:4306557-4304505	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00048	16825	18291	mdtP	0/0	100.0	99.9	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00123	68	973	mphA	0/0	100.0	100.0	D16251.1:2531-1625	The mphA gene encodes for resistance enzyme MPH(2’)-I which preferentially inactivate 14-membered macrolides (e.g.erythromycin telithromycin roxithromycin) over 16-membered macrolides (e.g.tylosin spiramycin). It phosphorylates macrolides at 2’-OH hydroxyl of desosamine sugar of macrolides in a GTP-dependent manner.	macrolide
contig00006	126902	127376	mphB	0/0	99.6	96.2	AE005174.2:3397370-3397847	The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides.	macrolide
contig00007	51471	53219	msbA	0/0	100.0	100.0	U00096.3:966620-968369	MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability.	nitroimidazole
contig00104	577	1407	OXA-1	0/0	100.0	100.0	JN420336.1:2230-1399	OXA-1 is a beta-lactamase found in E. coli	cephalosporin, penam
contig00001	156191	157159	pmrF	0/0	100.0	98.0	U00096:2367070-2368039	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide
contig00076	3807	4646	sul1	0/0	100.0	100.0	JF969163:1053-1893	Sul1 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria. It is linked to other resistance genes of class 1 integrons.	sulfonamide
contig00082	85	900	sul2	0/0	100.0	100.0	AY055428.1:21084-20268	Sul2 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria usually found on small plasmids.	sulfonamide
contig00074	176	1036	TEM-1	0/0	100.0	99.9	AL513383:161910-162771	TEM-1 is a broad-spectrum beta-lactamase found in many Gram-negative bacteria. Confers resistance to penicillins and first generation cephalosphorins.	cephalosporin, monobactam, penam, penem
contig00088	1998	3203	tet(B)	0/0	100.0	99.8	AB089595:0-1206	Tet(B) is a tetracycline efflux protein expressed in many Gram-negative bacteria. It confers resistance to tetracycline doxycycline and minocycline but not tigecycline.	tetracycline
contig00017	46587	48074	tolC	0/0	100.0	99.9	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan
contig00001	94315	95958	yojI	0/0	100.0	100.0	U00096.3:2308615-2306971	YojI mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. YojI is capable of pumping out microcin molecules. The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI.	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00094	33	893	(AGly)aac3-IId	0/0	100.0	99.9	EU022314:1-861	(AGly)aac3-IId	NA
contig00076	2472	3260	(AGly)aadA5	0/0	100.0	100.0	AF137361:64-852	(AGly)aadA5	NA
contig00082	5399	6178	(AGly)strA	0/0	97.0	99.9	AB366441:22458-23261	(AGly)strA	NA
contig00082	4563	5399	(AGly)strB	0/0	100.0	100.0	FJ474091:264-1100	(AGly)strB	NA
contig00001	334197	335495	(Bla)AmpC1_Ecoli	0/0	99.5	96.1	FN649414:2765051-2766355	(Bla)AmpC1_Ecoli	NA
contig00025	38370	39503	(Bla)AmpC2_Ecoli	0/0	100.0	97.3	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00002	127462	128619	(Bla)ampH_Ecoli	0/0	100.0	100.0	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00085	1871	2746	(Bla)blaCTX-M-15	0/0	100.0	100.0	JQ686199:261-1136	(Bla)blaCTX-M-15	NA
contig00104	577	1407	(Bla)blaOXA-1	0/0	100.0	100.0	JQ682867:1-831	(Bla)blaOXA-1	NA
contig00074	176	1036	(Bla)blaTEM-105	0/0	100.0	99.9	AF516720:215-1075	(Bla)blaTEM-105	NA
contig00023	9089	10990	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100.0	100.0	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA
contig00123	68	973	(MLS)mph(A)	0/0	100.0	100.0	DQ445270:1626-2531	(MLS)mph(A)	NA
contig00084	619	1278	(Phe)catA1	0/0	100.0	99.8	V00622:244-903	(Phe)catA1	NA
contig00076	3807	4646	(Sul)sul1	0/0	100.0	100.0	AF071413:6700-7539	(Sul)sul1	NA
contig00082	85	900	(Sul)sul2	0/0	100.0	100.0	EU360945:1617-2432	(Sul)sul2	NA
contig00088	1998	3203	(Tet)tetB	0/0	100.0	99.7	AB089594:1-1206	(Tet)tetB	NA
contig00076	1868	2341	(Tmt)dfrA17	0/0	100.0	100.0	AB126604:98-571	(Tmt)dfrA17	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00094	33	893	aac(3)-IId	0/0	100.0	100.0	NG_047251.1	aminoglycoside N-acetyltransferase AAC(3)-IId	GENTAMICIN
contig00104	1538	2092	aac(6’)-Ib-D181Y	0/0	100.0	99.8	NG_067946.1	AAC(6’)-Ib family aminoglycoside 6’-N-acetyltransferase	AMIKACIN, KANAMYCIN, TOBRAMYCIN
contig00076	2472	3260	aadA5	0/0	100.0	100.0	NG_047357.1	ANT(3’’)-Ia family aminoglycoside nucleotidyltransferase AadA5	STREPTOMYCIN
contig00082	5399	6178	aph(3’’)-Ib	0/0	94.2	100.0	NG_056002.2	aminoglycoside O-phosphotransferase APH(3’’)-Ib	STREPTOMYCIN
contig00082	4563	5399	aph(6)-Id	0/0	100.0	100.0	NG_047464.1	aminoglycoside O-phosphotransferase APH(6)-Id	STREPTOMYCIN
contig00085	1871	2746	blaCTX-M-15	0/0	100.0	100.0	NG_048935.1	class A extended-spectrum beta-lactamase CTX-M-15	CEPHALOSPORIN
contig00025	38370	39503	blaEC-15	0/0	100.0	98.5	NG_049081.1	class C extended-spectrum beta-lactamase EC-15	CEPHALOSPORIN
contig00104	577	1407	blaOXA-1	0/0	100.0	100.0	NG_049392.1	oxacillin-hydrolyzing class D beta-lactamase OXA-1	CEPHALOSPORIN
contig00074	176	1036	blaTEM-1	0/0	100.0	100.0	NG_050145.1	class A broad-spectrum beta-lactamase TEM-1	BETA-LACTAM
contig00084	619	1278	catA1	0/0	100.0	99.8	NG_047582.1	type A-1 chloramphenicol O-acetyltransferase	CHLORAMPHENICOL
contig00076	1868	2341	dfrA17	0/0	100.0	99.8	NG_047710.1	trimethoprim-resistant dihydrofolate reductase DfrA17	TRIMETHOPRIM
contig00123	68	989	mph(A)	1/1	100.0	99.7	NG_047986.1	Mph(A) family macrolide 2’-phosphotransferase	MACROLIDE
contig00076	3807	4646	sul1	0/0	100.0	100.0	NG_048082.1	sulfonamide-resistant dihydropteroate synthase Sul1	SULFONAMIDE
contig00082	85	900	sul2	0/0	100.0	100.0	NG_051852.1	sulfonamide-resistant dihydropteroate synthase Sul2	SULFONAMIDE
contig00088	1998	3203	tet(B)	0/0	100.0	100.0	NG_048163.1	tetracycline efflux MFS transporter Tet(B)	TETRACYCLINE

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00094	33	893	AAC3	0/0	100.0	100.0	MEG_64	Drugs:Aminoglycosides:Aminoglycoside_N-acetyltransferases:AAC3	NA
contig00002	38130	39323	ACRA	0/0	100.0	100.0	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00002	39346	42495	ACRB	0/0	100.0	100.0	MEG_401	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRB	NA
contig00006	148083	151196	ACRD	0/0	100.0	98.8	MEG_407	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ACRD	NA
contig00075	5854	8958	ACRF	0/0	100.0	100.0	MEG_409	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRF	NA
contig00056	20506	21168	ACRS	0/0	100.0	100.0	MEG_415	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS	NA
contig00002	127462	128619	AMPH	0/0	100.0	100.0	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00076	2472	3260	ANT3-DPRIME	0/0	100.0	100.0	MEG_928	Drugs:Aminoglycosides:Aminoglycoside_O-nucleotidyltransferases:ANT3-DPRIME	NA
contig00082	5399	6178	APH3-DPRIME	0/0	94.2	100.0	MEG_1019	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH3-DPRIME	NA
contig00082	4563	5399	APH6	0/0	100.0	100.0	MEG_1086	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH6	NA
contig00061	11601	13454	ASMA	0/0	100.0	96.8	MEG_1180	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:ASMA	NA
contig00017	70351	71170	BACA	0/0	99.8	98.8	MEG_1189	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00072	10538	11260	BAER	0/0	100.0	99.3	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00072	9138	10541	BAES	0/0	100.0	98.7	MEG_1193	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES	NA
contig00001	67338	68528	BCR	0/0	100.0	99.9	MEG_1210	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR	NA
contig00025	38370	39503	BLAEC	0/0	100.0	98.5	MEG_1282	Drugs:betalactams:Class_C_betalactamases:BLAEC	NA
contig00084	608	1278	CATA	0/0	100.0	100.0	MEG_1593	Drugs:Phenicol:Chloramphenicol_acetyltransferases:CATA	NA
contig00013	60881	61579	CPXAR	0/0	100.0	100.0	MEG_2122	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00013	61576	62949	CPXAR	0/0	100.0	100.0	MEG_2121	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00010	15081	15713	CRP	0/0	100.0	99.7	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00023	12	954	CTX	0/0	100.0	98.2	MEG_2435	Drugs:betalactams:Class_A_betalactamases:CTX	NA
contig00076	1868	2341	DFRA	0/0	100.0	100.0	MEG_2547	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00012	47169	48341	EMRA	0/0	100.0	97.9	MEG_2722	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA	NA
contig00012	48358	49896	EMRB	0/0	100.0	98.6	MEG_2725	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRB	NA
contig00034	43175	44365	EMRD	0/0	100.0	100.0	MEG_2729	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD	NA
contig00001	270703	271866	EMRK	0/0	100.0	98.2	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig00012	46512	47042	EMRR	0/0	100.0	99.4	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00001	269165	270703	EMRY	0/0	100.0	97.7	MEG_2736	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRY	NA
contig00018	67027	68670	EPTA	0/0	100.0	99.9	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig00001	272901	276494	EVGS	0/0	100.0	97.2	MEG_2869	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EVGS	NA
contig00037	1784	2512	GADW	0/0	100.0	100.0	MEG_3081	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig00037	592	1416	GADX	0/0	100.0	99.9	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00033	5236	5649	HNS	0/0	100.0	99.3	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00030	8102	8779	KDPE	0/0	100.0	100.0	MEG_3448	Drugs:Aminoglycosides:Aminoglycoside_efflux_pumps:KDPE	NA
contig00004	184592	184981	MARA	0/0	100.0	100.0	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00004	184995	185429	MARR	0/0	100.0	100.0	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00008	30177	31409	MDFA	0/0	100.0	100.0	MEG_3737	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDFA	NA
contig00072	278	1525	MDTA	0/0	100.0	98.0	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00072	1525	4647	MDTB	0/0	100.0	97.0	MEG_3747	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTB	NA
contig00072	4648	7725	MDTC	0/0	100.0	97.7	MEG_3749	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTC	NA
contig00037	6013	7170	MDTE	0/0	100.0	100.0	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00037	2875	5988	MDTF	0/0	100.0	100.0	MEG_3752	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTF	NA
contig00032	18399	19625	MDTG	0/0	100.0	100.0	MEG_3753	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig00032	28254	29462	MDTH	0/0	100.0	99.9	MEG_3755	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTH	NA
contig00004	151870	152199	MDTI	0/0	100.0	100.0	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00004	151518	151883	MDTJ	0/0	100.0	99.5	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00004	80116	81489	MDTK	0/0	100.0	100.0	MEG_3759	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:MDTK	NA
contig00044	3939	5171	MDTM	0/0	100.0	100.0	MEG_3761	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTM	NA
contig00048	20339	21370	MDTN	0/0	100.0	100.0	MEG_3763	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN	NA
contig00048	18288	20339	MDTO	0/0	100.0	100.0	MEG_3764	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTO	NA
contig00048	16825	18291	MDTP	0/0	100.0	99.9	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig00123	68	989	MPHA	1/1	100.0	99.7	MEG_4030	Drugs:MLS:Macrolide_phosphotransferases:MPHA	NA
contig00006	126902	127376	MPHB	0/0	99.6	96.2	MEG_4033	Drugs:MLS:Macrolide_phosphotransferases:MPHB	NA
contig00007	51471	53219	MSBA	0/0	100.0	100.0	MEG_4061	Drugs:Multi-drug_resistance:Multi-drug_ABC_efflux_pumps:MSBA	NA
contig00019	2074	2406	MVRC	0/0	100.0	91.9	MEG_4103	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MVRC	NA
contig00104	577	1407	OXA	0/0	100.0	100.0	MEG_4980	Drugs:betalactams:Class_D_betalactamases:OXA	NA
contig00023	9089	10990	PBP2	0/0	100.0	100.0	MEG_5400	Drugs:betalactams:Penicillin_binding_protein:PBP2	NA
contig00001	334197	335495	PBP4B	0/0	99.5	96.1	MEG_5409	Drugs:betalactams:Penicillin_binding_protein:PBP4B	NA
contig00001	156191	157159	PMRF	0/0	100.0	98.0	MEG_5801	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF	NA
contig00038	21724	22593	ROBA	0/0	100.0	99.0	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00041	35222	35545	SOXS	0/0	100.0	100.0	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00076	3806	4773	SULI	0/0	100.0	100.0	MEG_6615	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULI	NA
contig00082	85	900	SULII	0/0	100.0	100.0	MEG_6617	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULII	NA
contig00088	1998	3203	TETB	0/0	100.0	100.0	MEG_7052	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETB	NA
contig00088	3997	4408	TETD	0/0	98.8	100.0	MEG_7070	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETD	NA
contig00001	94315	95958	YOGI	0/0	100.0	100.0	MEG_7842	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:YOGI	NA

ID044

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00104	901	1702	aadA2_1	0/0	97.9	99.9	NC_010870	aadA2	Streptomycin
contig00108	5421	6200	aph(3’’)-Ib_5	0/0	97.0	100.0	AF321551	aph(3’’)-Ib	Streptomycin
contig00108	4585	5421	aph(6)-Id_1	0/0	100.0	100.0	M28829	aph(6)-Id	Streptomycin
contig00111	2475	3350	blaCTX-M-15_1	0/0	100.0	100.0	AY044436	blaCTX-M-15	Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig00116	3851	4461	catA1_1	0/0	92.6	99.8	V00622	catA1	Chloramphenicol
contig00104	6	503	dfrA12_8	0/0	100.0	100.0	AM040708	dfrA12	Trimethoprim
contig00133	263	1026	erm(B)_18	2/2	100.0	99.0	X66468	erm(B)	Erythromycin, Lincomycin, Clindamycin, Quinupristin, Pristinamycin_IA, Virginiamycin_S
contig00001	10012	11244	mdf(A)_1	0/0	100.0	99.9	Y08743	mdf(A)
contig00158	68	998	mph(A)_2	2/10	100.0	98.7	U36578	mph(A)	Erythromycin, Azithromycin, Spiramycin, Telithromycin
contig00104	2180	3046	sul1_5	0/0	100.0	99.9	EU780013	sul1	Sulfamethoxazole
contig00108	85	900	sul2_2	0/0	100.0	100.0	AY034138	sul2	Sulfamethoxazole
contig00127	850	2055	tet(B)_2	0/0	100.0	100.0	AF326777	tet(B)	Doxycycline, Tetracycline, Minocycline

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00104	923	1702	aadA2	0/0	100.0	99.9	AF156486:5012-5792	aadA2 is an aminoglycoside nucleotidyltransferase gene encoded by plasmids and integrons in K. pneumoniae Salmonella spp. Corynebacterium glutamicum C. freundii and Aeromonas spp.	aminoglycoside
contig00005	38757	41906	acrB	0/0	100.0	100.0	U00096.3:484403-481253	Protein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug/proton antiporter.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00002	135351	138464	acrD	0/0	100.0	100.0	AP009048.1:2586250-2589364	AcrD is an aminoglycoside efflux pump expressed in E. coli. Its expression can be induced by indole and is regulated by baeRS and cpxAR.	aminoglycoside
contig00020	8641	9798	acrE	0/0	100.0	99.9	U00096:3413863-3415021	AcrE is a membrane fusion protein similar to AcrA.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00020	5525	8629	acrF	0/0	100.0	100.0	U00096:3415032-3418137	AcrF is a inner membrane transporter similar to AcrB.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00020	10197	10859	acrS	0/0	100.0	100.0	U00096:3413465-3412802	AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.	cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00108	5421	6200	APH(3’’)-Ib	0/0	97.0	99.7	AF313472:15593-16397	APH(3’’)-Ib is an aminoglycoside phosphotransferase encoded by plasmids transposons integrative conjugative elements and chromosomes in Enterobacteriaceae and Pseudomonas spp.	aminoglycoside
contig00108	4585	5421	APH(6)-Id	0/0	100.0	99.9	AF024602:3155-3992	APH(6)-Id is an aminoglycoside phosphotransferase encoded by plasmids integrative conjugative elements and chromosomal genomic islands in K. pneumoniae Salmonella spp. E. coli Shigella flexneri Providencia alcalifaciens Pseudomonas spp. V. cholerae Edwardsiella tarda Pasteurella multocida and Aeromonas bestiarum	aminoglycoside
contig00096	7786	8607	bacA	0/0	100.0	98.7	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00023	223	945	baeR	0/0	100.0	99.3	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00023	942	2345	baeS	0/0	100.0	98.7	AP009048:2165012-2166416	BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.	aminocoumarin, aminoglycoside
contig00116	3851	4461	catI	0/0	92.6	99.8	V00622:243-903	catI is a chromosome and transposon-encoded variant of the cat gene found in Escherichia coli and Acinetobacter baumannii	phenicol
contig00007	61493	62866	cpxA	0/0	100.0	99.0	BA000007.3:4905062-4903688	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	aminocoumarin, aminoglycoside
contig00006	2640	3272	CRP	0/0	100.0	99.4	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00111	2475	3350	CTX-M-15	0/0	100.0	100.0	AY044436:1435-2311	CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family	cephalosporin
contig00104	6	503	dfrA12	0/0	100.0	100.0	GU585907.1:22103-21605	dfrA12 is an integron-encoded dihydrofolate reductase found in Vibrio cholerae	diaminopyrimidine
contig00014	19864	21036	emrA	0/0	100.0	100.0	AP009048:2810082-2811255	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	fluoroquinolone
contig00014	21053	22591	emrB	0/0	100.0	100.0	U00096:2812615-2814154	emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin.	fluoroquinolone
contig00044	26582	27637	emrK	0/0	100.0	99.9	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00014	19207	19737	emrR	0/0	100.0	99.8	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00044	25044	26582	emrY	0/0	100.0	99.9	D78168:1591-3130	emrY is a multidrug transport that moves substrates across the inner membrane of the Gram-negative E. coli. It is a homolog of emrB.	tetracycline
contig00010	99938	101581	eptA	0/0	100.0	99.9	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00133	289	1034	ErmB	1/1	99.9	99.2	AF242872.1:2131-2878	ErmB confers the MLSb phenotype. Similar to ErmC expression of ErmB is inducible by erythromycin. The leader peptide causes attenuation of the mRNA and stabilizes the structure preventing further translation. When erythromycin is present it binds the leader peptide causing a change in conformation allowing for the expression of ErmB.	lincosamide, macrolide, streptogramin
contig00005	37541	38734	Escherichia_coli_acrA	0/0	100.0	100.0	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00010	65397	66530	Escherichia_coli_ampC	0/0	100.0	97.3	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00002	169863	171167	Escherichia_coli_ampC1_beta-lactamase	0/0	100.0	99.9	FN649414.1:2765050-2766355	An ampC-like beta-lactamase identified from Escherichia coli.	cephalosporin, penam
contig00005	126769	127926	Escherichia_coli_ampH	0/0	100.0	100.0	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig00001	10012	11244	Escherichia_coli_mdfA	0/0	100.0	98.4	JQ394987:0-1233	Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter.	benzalkonium_chloride, rhodamine, tetracycline
contig00044	28160	28774	evgA	0/0	100.0	100.0	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00044	28779	32372	evgS	0/0	100.0	100.0	U00096:2484373-2487967	EvgS is a sensor protein that phosphorylates the regulatory protein EvgA. evgS corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	fluoroquinolone, macrolide, penam, tetracycline
contig00037	2242	2970	gadW	0/0	100.0	94.7	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig00037	1051	1875	gadX	0/0	100.0	100.0	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00024	18847	19260	H-NS	0/0	100.0	99.3	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00008	8154	8831	kdpE	0/0	100.0	100.0	U00096.3:721733-721055	kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding.	aminoglycoside
contig00056	22979	23362	marA	0/0	100.0	100.0	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00023	9958	11205	mdtA	0/0	100.0	97.0	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00023	6836	9958	mdtB	0/0	100.0	96.9	U00096:2155262-2158385	MdtB is a transporter that forms a heteromultimer complex with MdtC to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex.	aminocoumarin
contig00023	3758	6835	mdtC	0/0	100.0	97.7	U00096:2158385-2161463	MdtC is a transporter that forms a heteromultimer complex with MdtB to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex. In the absence of MdtB MdtC can form a homomultimer complex that results in a functioning efflux complex with a narrower drug specificity. mdtC corresponds to 3 loci in Pseudomonas aeruginosa PAO1 (gene name: muxC/muxB) and 3 loci in Pseudomonas aeruginosa LESB58.	aminocoumarin
contig00037	6471	7628	mdtE	0/0	100.0	100.0	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00037	3333	6446	mdtF	0/0	100.0	100.0	U00096:3660413-3663527	MdtF is the multidrug inner membrane transporter for the MdtEF-TolC efflux complex.	fluoroquinolone, macrolide, penam
contig00026	18399	19625	mdtG	0/0	100.0	99.4	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00026	28254	29462	mdtH	0/0	100.0	100.0	U00096:1125326-1124117	Multidrug resistance protein MdtH	fluoroquinolone
contig00076	473	1684	mdtM	0/0	98.3	95.5	U00096.3:4568519-4567286	Multidrug resistance protein MdtM	acridine_dye, fluoroquinolone, lincosamide, nucleoside, phenicol
contig00021	10920	11951	mdtN	0/0	100.0	100.0	AP009048.1:4307588-4306556	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	acridine_dye, nucleoside
contig00021	11951	14002	mdtO	0/0	100.0	100.0	AP009048.1:4306557-4304505	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00021	13999	15465	mdtP	0/0	100.0	100.0	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00158	68	970	mphA	0/0	99.7	100.0	D16251.1:2531-1625	The mphA gene encodes for resistance enzyme MPH(2’)-I which preferentially inactivate 14-membered macrolides (e.g.erythromycin telithromycin roxithromycin) over 16-membered macrolides (e.g.tylosin spiramycin). It phosphorylates macrolides at 2’-OH hydroxyl of desosamine sugar of macrolides in a GTP-dependent manner.	macrolide
contig00002	114189	114665	mphB	0/0	100.0	98.3	AE005174.2:3397370-3397847	The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides.	macrolide
contig00001	92960	94708	msbA	0/0	100.0	100.0	U00096.3:966620-968369	MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability.	nitroimidazole
contig00019	17275	18243	pmrF	0/0	100.0	100.0	U00096:2367070-2368039	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide
contig00104	2207	3046	sul1	0/0	100.0	100.0	JF969163:1053-1893	Sul1 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria. It is linked to other resistance genes of class 1 integrons.	sulfonamide
contig00108	85	900	sul2	0/0	100.0	100.0	AY055428.1:21084-20268	Sul2 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria usually found on small plasmids.	sulfonamide
contig00127	850	2055	tet(B)	0/0	100.0	99.8	AB089595:0-1206	Tet(B) is a tetracycline efflux protein expressed in many Gram-negative bacteria. It confers resistance to tetracycline doxycycline and minocycline but not tigecycline.	tetracycline
contig00015	56955	58442	tolC	0/0	100.0	99.7	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan
contig00036	42513	44156	yojI	0/0	100.0	100.0	U00096.3:2308615-2306971	YojI mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. YojI is capable of pumping out microcin molecules. The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI.	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00104	923	1702	(AGly)aadA2	0/0	100.0	99.9	X68227:66-945	(AGly)aadA2	NA
contig00108	5421	6200	(AGly)strA	0/0	97.0	99.9	AB366441:22458-23261	(AGly)strA	NA
contig00108	4585	5421	(AGly)strB	0/0	100.0	100.0	FJ474091:264-1100	(AGly)strB	NA
contig00002	169863	171167	(Bla)AmpC1_Ecoli	0/0	100.0	99.9	FN649414:2765051-2766355	(Bla)AmpC1_Ecoli	NA
contig00010	65397	66530	(Bla)AmpC2_Ecoli	0/0	100.0	97.3	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00005	126769	127926	(Bla)ampH_Ecoli	0/0	100.0	100.0	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00111	2475	3350	(Bla)blaCTX-M-15	0/0	100.0	100.0	JQ686199:261-1136	(Bla)blaCTX-M-15	NA
contig00008	60241	62142	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100.0	100.0	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA
contig00133	289	1026	(MLS)erm(B)	0/0	100.0	99.6	M11180:714-1451	(MLS)erm(B)	NA
contig00158	68	970	(MLS)mph(A)	0/0	99.7	100.0	DQ445270:1626-2531	(MLS)mph(A)	NA
contig00116	3851	4461	(Phe)catA1	0/0	92.6	99.8	V00622:244-903	(Phe)catA1	NA
contig00104	2207	3046	(Sul)sul1	0/0	100.0	100.0	AF071413:6700-7539	(Sul)sul1	NA
contig00108	85	900	(Sul)sul2	0/0	100.0	100.0	EU360945:1617-2432	(Sul)sul2	NA
contig00127	850	2055	(Tet)tetB	0/0	100.0	99.7	AB089594:1-1206	(Tet)tetB	NA
contig00104	6	503	(Tmt)dfrA12	0/0	100.0	100.0	Z21672:310-807	(Tmt)dfrA12	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00104	911	1702	aadA2	0/0	100.0	100.0	NG_047343.1	ANT(3’’)-Ia family aminoglycoside nucleotidyltransferase AadA2	STREPTOMYCIN
contig00108	5421	6200	aph(3’’)-Ib	0/0	94.2	100.0	NG_056002.2	aminoglycoside O-phosphotransferase APH(3’’)-Ib	STREPTOMYCIN
contig00108	4585	5421	aph(6)-Id	0/0	100.0	100.0	NG_047464.1	aminoglycoside O-phosphotransferase APH(6)-Id	STREPTOMYCIN
contig00111	2475	3350	blaCTX-M-15	0/0	100.0	100.0	NG_048935.1	class A extended-spectrum beta-lactamase CTX-M-15	CEPHALOSPORIN
contig00010	65397	66530	blaEC-15	0/0	100.0	98.5	NG_049081.1	class C extended-spectrum beta-lactamase EC-15	CEPHALOSPORIN
contig00116	3851	4461	catA1	0/0	92.6	99.8	NG_047582.1	type A-1 chloramphenicol O-acetyltransferase	CHLORAMPHENICOL
contig00104	6	503	dfrA12	0/0	100.0	100.0	NG_047689.1	trimethoprim-resistant dihydrofolate reductase DfrA12	TRIMETHOPRIM
contig00133	289	1026	erm(B)	0/0	100.0	99.9	NG_047804.1	23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(B)	MACROLIDE
contig00158	68	998	mph(A)	2/10	100.0	98.7	NG_047986.1	Mph(A) family macrolide 2’-phosphotransferase	MACROLIDE
contig00104	2207	3046	sul1	0/0	100.0	100.0	NG_048082.1	sulfonamide-resistant dihydropteroate synthase Sul1	SULFONAMIDE
contig00108	85	900	sul2	0/0	100.0	100.0	NG_051852.1	sulfonamide-resistant dihydropteroate synthase Sul2	SULFONAMIDE
contig00127	850	2055	tet(B)	0/0	100.0	100.0	NG_048163.1	tetracycline efflux MFS transporter Tet(B)	TETRACYCLINE

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00005	37541	38734	ACRA	0/0	100.0	100.0	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00005	38757	41906	ACRB	0/0	100.0	100.0	MEG_401	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRB	NA
contig00002	135351	138464	ACRD	0/0	100.0	100.0	MEG_407	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ACRD	NA
contig00020	8641	9798	ACRE	0/0	100.0	99.9	MEG_408	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRE	NA
contig00020	5525	8629	ACRF	0/0	100.0	100.0	MEG_409	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRF	NA
contig00020	10197	10859	ACRS	0/0	100.0	100.0	MEG_415	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS	NA
contig00005	126769	127926	AMPH	0/0	100.0	100.0	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00104	901	1702	ANT3-DPRIME	0/0	97.9	99.9	MEG_975	Drugs:Aminoglycosides:Aminoglycoside_O-nucleotidyltransferases:ANT3-DPRIME	NA
contig00108	5421	6200	APH3-DPRIME	0/0	94.2	100.0	MEG_1019	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH3-DPRIME	NA
contig00108	4585	5421	APH6	0/0	100.0	100.0	MEG_1086	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH6	NA
contig00023	23136	24989	ASMA	0/0	100.0	95.7	MEG_1180	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:ASMA	NA
contig00096	7786	8607	BACA	0/0	100.0	98.9	MEG_1189	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00023	223	945	BAER	0/0	100.0	99.3	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00023	942	2345	BAES	0/0	100.0	98.7	MEG_1193	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES	NA
contig00012	67340	68530	BCR	0/0	100.0	99.9	MEG_1210	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR	NA
contig00010	65397	66530	BLAEC	0/0	100.0	98.5	MEG_1282	Drugs:betalactams:Class_C_betalactamases:BLAEC	NA
contig00116	3851	4461	CATA	0/0	92.6	100.0	MEG_1584	Drugs:Phenicol:Chloramphenicol_acetyltransferases:CATA	NA
contig00007	60798	61496	CPXAR	0/0	100.0	100.0	MEG_2122	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00007	61493	62866	CPXAR	0/0	100.0	100.0	MEG_2121	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00006	2640	3272	CRP	0/0	100.0	99.4	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00079	12915	13857	CTX	0/0	100.0	98.2	MEG_2435	Drugs:betalactams:Class_A_betalactamases:CTX	NA
contig00104	6	503	DFRA	0/0	100.0	100.0	MEG_2551	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00014	19864	21036	EMRA	0/0	100.0	100.0	MEG_2722	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA	NA
contig00014	21053	22591	EMRB	0/0	100.0	100.0	MEG_2725	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRB	NA
contig00004	87250	88440	EMRD	0/0	100.0	100.0	MEG_2729	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD	NA
contig00044	26582	27745	EMRK	0/0	100.0	99.9	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig00014	19207	19737	EMRR	0/0	100.0	99.8	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00044	25044	26582	EMRY	0/0	100.0	99.9	MEG_2736	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRY	NA
contig00010	99938	101581	EPTA	0/0	100.0	99.9	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig00133	263	1026	ERMB	2/2	100.0	99.0	MEG_2801	Drugs:MLS:23S_rRNA_methyltransferases:ERMB	NA
contig00044	28779	32372	EVGS	0/0	100.0	100.0	MEG_2870	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EVGS	NA
contig00037	2242	2970	GADW	0/0	100.0	100.0	MEG_3081	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig00037	1051	1875	GADX	0/0	100.0	100.0	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00024	18847	19260	HNS	0/0	100.0	99.3	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00008	8154	8831	KDPE	0/0	100.0	100.0	MEG_3448	Drugs:Aminoglycosides:Aminoglycoside_efflux_pumps:KDPE	NA
contig00056	22973	23362	MARA	0/0	100.0	100.0	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00056	22525	22959	MARR	0/0	100.0	100.0	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00001	10012	11244	MDFA	0/0	100.0	100.0	MEG_3737	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDFA	NA
contig00023	9958	11205	MDTA	0/0	100.0	97.0	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00023	6836	9958	MDTB	0/0	100.0	96.9	MEG_3747	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTB	NA
contig00023	3758	6835	MDTC	0/0	100.0	97.7	MEG_3749	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTC	NA
contig00037	6471	7628	MDTE	0/0	100.0	100.0	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00037	3333	6446	MDTF	0/0	100.0	100.0	MEG_3752	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTF	NA
contig00026	18399	19625	MDTG	0/0	100.0	100.0	MEG_3753	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig00026	28254	29462	MDTH	0/0	100.0	100.0	MEG_3755	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTH	NA
contig00053	1572	1901	MDTI	0/0	100.0	100.0	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00053	1220	1585	MDTJ	0/0	100.0	99.5	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00009	57987	59360	MDTK	0/0	100.0	100.0	MEG_3759	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:MDTK	NA
contig00076	473	1684	MDTM	0/0	98.3	95.5	MEG_3761	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTM	NA
contig00021	10920	11951	MDTN	0/0	100.0	100.0	MEG_3763	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN	NA
contig00021	11951	14002	MDTO	0/0	100.0	100.0	MEG_3764	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTO	NA
contig00021	13999	15465	MDTP	0/0	100.0	100.0	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig00158	68	998	MPHA	2/10	100.0	98.7	MEG_4030	Drugs:MLS:Macrolide_phosphotransferases:MPHA	NA
contig00002	114189	114665	MPHB	0/0	100.0	98.3	MEG_4033	Drugs:MLS:Macrolide_phosphotransferases:MPHB	NA
contig00001	92960	94708	MSBA	0/0	100.0	100.0	MEG_4061	Drugs:Multi-drug_resistance:Multi-drug_ABC_efflux_pumps:MSBA	NA
contig00008	60241	62142	PBP2	0/0	100.0	100.0	MEG_5400	Drugs:betalactams:Penicillin_binding_protein:PBP2	NA
contig00002	169863	171167	PBP4B	0/0	100.0	99.9	MEG_5409	Drugs:betalactams:Penicillin_binding_protein:PBP4B	NA
contig00019	17275	18243	PMRF	0/0	100.0	100.0	MEG_5801	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF	NA
contig00003	19976	20845	ROBA	0/0	100.0	99.0	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00021	37082	37405	SOXS	0/0	100.0	100.0	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00104	2206	3173	SULI	0/0	100.0	100.0	MEG_6615	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULI	NA
contig00108	85	900	SULII	0/0	100.0	100.0	MEG_6617	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULII	NA
contig00127	850	2055	TETB	0/0	100.0	100.0	MEG_7052	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETB	NA
contig00036	42513	44156	YOGI	0/0	100.0	100.0	MEG_7842	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:YOGI	NA

ID046II

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00120	692	1495	aph(3’’)-Ib_5	0/0	100.0	100	AF321551	aph(3’’)-Ib	Streptomycin
contig00023	13083	13958	blaCTX-M-15_1	0/0	100.0	100	AY044436	blaCTX-M-15	Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig00367	823	1683	blaTEM-1B_1	0/0	100.0	100	AY458016	blaTEM-1B	Amoxicillin, Ampicillin, Cephalothin, Piperacillin, Ticarcillin
contig00023	7786	8442	qnrS1_1	0/0	100.0	100	AB187515	qnrS1	Ciprofloxacin
contig00120	1556	2371	sul2_2	0/0	100.0	100	AY034138	sul2	Sulfamethoxazole
contig00470	1348	2594	tet(A)_6	0/0	97.8	100	AF534183	tet(A)	Doxycycline, Tetracycline

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00072	3690	4847	acrE	0/0	100.0	99.0	U00096:3413863-3415021	AcrE is a membrane fusion protein similar to AcrA.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00072	2630	3292	acrS	0/0	100.0	99.1	U00096:3413465-3412802	AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.	cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00120	692	1495	APH(3’’)-Ib	0/0	100.0	99.8	AF313472:15593-16397	APH(3’’)-Ib is an aminoglycoside phosphotransferase encoded by plasmids transposons integrative conjugative elements and chromosomes in Enterobacteriaceae and Pseudomonas spp.	aminoglycoside
contig00252	2259	3080	bacA	0/0	100.0	100.0	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00041	2930	3652	baeR	0/0	100.0	100.0	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00041	1530	2933	baeS	0/0	100.0	100.0	AP009048:2165012-2166416	BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.	aminocoumarin, aminoglycoside
contig00933	402	1034	CRP	0/0	100.0	99.4	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00023	13083	13958	CTX-M-15	0/0	100.0	100.0	AY044436:1435-2311	CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family	cephalosporin
contig00264	2851	4023	emrA	0/0	100.0	98.1	AP009048:2810082-2811255	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	fluoroquinolone
contig00264	1296	2834	emrB	0/0	100.0	99.3	U00096:2812615-2814154	emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin.	fluoroquinolone
contig00258	2693	3748	emrK	0/0	100.0	99.9	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00672	26	556	emrR	0/0	100.0	100.0	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00258	1155	2693	emrY	0/0	100.0	99.0	D78168:1591-3130	emrY is a multidrug transport that moves substrates across the inner membrane of the Gram-negative E. coli. It is a homolog of emrB.	tetracycline
contig00306	1290	2483	Escherichia_coli_acrA	0/0	100.0	100.0	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00361	2079	3236	Escherichia_coli_ampH	0/0	100.0	98.9	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig00924	317	649	Escherichia_coli_emrE	0/0	100.0	92.2	Z11877.1:485-818	Member of the small MDR (multidrug resistance) family of transporters, in Escherichia coli this protein provides resistance against a number of positively charged compounds including ethidium bromide and erythromycin, proton-dependent secondary transporter which exchanges protons for compound translocation	macrolide
contig02169	3	617	evgA	0/0	100.0	100.0	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00373	1	3359	evgS	0/0	93.5	100.0	U00096:2484373-2487967	EvgS is a sensor protein that phosphorylates the regulatory protein EvgA. evgS corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	fluoroquinolone, macrolide, penam, tetracycline
contig00113	20	748	gadW	0/0	100.0	95.5	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig01389	535	1311	gadX	0/0	94.2	99.7	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00273	2921	3598	kdpE	0/0	100.0	99.0	U00096.3:721733-721055	kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding.	aminoglycoside
contig01107	469	1601	mdtA	0/0	90.8	97.5	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00113	4249	5406	mdtE	0/0	100.0	99.6	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00113	1111	4224	mdtF	0/0	100.0	98.4	U00096:3660413-3663527	MdtF is the multidrug inner membrane transporter for the MdtEF-TolC efflux complex.	fluoroquinolone, macrolide, penam
contig00416	439	1647	mdtH	0/0	100.0	97.9	U00096:1125326-1124117	Multidrug resistance protein MdtH	fluoroquinolone
contig01074	135	1166	mdtN	0/0	100.0	100.0	AP009048.1:4307588-4306556	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	acridine_dye, nucleoside
contig00324	2523	2999	mphB	0/0	100.0	98.3	AE005174.2:3397370-3397847	The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides.	macrolide
contig00111	943	2691	msbA	0/0	100.0	99.9	U00096.3:966620-968369	MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability.	nitroimidazole
contig00023	7786	8442	QnrS1	0/0	100.0	100.0	DQ485529.1:0-657	QnrS1 is a plasmid-mediated quinolone resistance protein found in Shigella flexneri	fluoroquinolone
contig00120	1556	2371	sul2	0/0	100.0	100.0	AY055428.1:21084-20268	Sul2 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria usually found on small plasmids.	sulfonamide
contig00367	823	1683	TEM-1	0/0	100.0	99.9	AL513383:161910-162771	TEM-1 is a broad-spectrum beta-lactamase found in many Gram-negative bacteria. Confers resistance to penicillins and first generation cephalosphorins.	cephalosporin, monobactam, penam, penem
contig00470	1348	2594	tet(A)	0/0	97.8	100.0	AF534183.1:2970-4245	TetA is a tetracycline efflux pump found in many species of Gram-negative bacteria.	tetracycline
contig00365	1826	3313	tolC	0/0	100.0	99.7	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan
contig00002	35344	36510	ugd	0/0	100.0	98.4	U00096:2099613-2098446	PmrE is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00120	692	1495	(AGly)strA	0/0	100	99.9	AB366441:22458-23261	(AGly)strA	NA
contig00361	2079	3236	(Bla)ampH_Ecoli	0/0	100	98.9	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00023	13083	13958	(Bla)blaCTX-M-15	0/0	100	100.0	JQ686199:261-1136	(Bla)blaCTX-M-15	NA
contig00367	823	1683	(Bla)blaTEM-105	0/0	100	99.9	AF516720:215-1075	(Bla)blaTEM-105	NA
contig00023	7786	8442	(Flq)qnr-S1	0/0	100	100.0	AB187515:9737-10393	(Flq)qnr-S1	NA
contig00120	1556	2371	(Sul)sul2	0/0	100	100.0	EU360945:1617-2432	(Sul)sul2	NA
contig00470	1320	2594	(Tet)tetA	0/0	100	100.0	JX424423:94438-95712	(Tet)tetA	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00120	692	1519	aph(3’’)-Ib	0/0	100	100	NG_056002.2	aminoglycoside O-phosphotransferase APH(3’’)-Ib	STREPTOMYCIN
contig00023	13083	13958	blaCTX-M-15	0/0	100	100	NG_048935.1	class A extended-spectrum beta-lactamase CTX-M-15	CEPHALOSPORIN
contig00367	823	1683	blaTEM-1	0/0	100	100	NG_050145.1	class A broad-spectrum beta-lactamase TEM-1	BETA-LACTAM
contig00023	7786	8442	qnrS1	0/0	100	100	NG_050543.1	quinolone resistance pentapeptide repeat protein QnrS1	QUINOLONE
contig00120	1556	2371	sul2	0/0	100	100	NG_051852.1	sulfonamide-resistant dihydropteroate synthase Sul2	SULFONAMIDE
contig00470	1320	2519	tet(A)	0/0	100	100	NG_048154.1	tetracycline efflux MFS transporter Tet(A)	TETRACYCLINE

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00306	1290	2483	ACRA	0/0	100.0	100.0	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00072	3690	4847	ACRE	0/0	100.0	99.0	MEG_408	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRE	NA
contig00072	2630	3292	ACRS	0/0	100.0	99.1	MEG_415	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS	NA
contig00361	2079	3236	AMPH	0/0	100.0	98.9	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00120	692	1519	APH3-DPRIME	0/0	100.0	100.0	MEG_1019	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH3-DPRIME	NA
contig00827	94	1946	ASMA	0/0	100.0	97.2	MEG_1180	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:ASMA	NA
contig00252	2259	3080	BACA	0/0	100.0	100.0	MEG_1190	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00041	2930	3652	BAER	0/0	100.0	100.0	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00041	1530	2933	BAES	0/0	100.0	100.0	MEG_1193	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES	NA
contig00235	1119	2309	BCR	0/0	100.0	100.0	MEG_1210	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR	NA
contig00933	402	1034	CRP	0/0	100.0	99.4	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig01998	18	869	CTX	0/0	92.2	95.3	MEG_2378	Drugs:betalactams:Class_A_betalactamases:CTX	NA
contig00264	2851	4023	EMRA	0/0	100.0	98.1	MEG_2722	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA	NA
contig00264	1296	2834	EMRB	0/0	100.0	99.3	MEG_2725	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRB	NA
contig00258	2693	3856	EMRK	0/0	100.0	99.9	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig00672	26	556	EMRR	0/0	100.0	100.0	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00258	1155	2693	EMRY	0/0	100.0	99.1	MEG_2736	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRY	NA
contig00373	1	3359	EVGS	0/0	93.5	100.0	MEG_2870	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EVGS	NA
contig00113	20	748	GADW	0/0	100.0	97.1	MEG_3081	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig01389	535	1311	GADX	0/0	94.2	99.7	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00273	2921	3598	KDPE	0/0	100.0	99.0	MEG_3448	Drugs:Aminoglycosides:Aminoglycoside_efflux_pumps:KDPE	NA
contig01107	469	1601	MDTA	0/0	90.8	97.5	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00113	4249	5406	MDTE	0/0	100.0	99.6	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00113	1111	4224	MDTF	0/0	100.0	98.4	MEG_3752	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTF	NA
contig00416	439	1647	MDTH	0/0	100.0	97.9	MEG_3755	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTH	NA
contig00474	508	837	MDTI	0/0	100.0	99.4	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00474	156	521	MDTJ	0/0	100.0	98.9	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig01074	135	1166	MDTN	0/0	100.0	100.0	MEG_3763	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN	NA
contig00324	2523	2999	MPHB	0/0	100.0	98.3	MEG_4033	Drugs:MLS:Macrolide_phosphotransferases:MPHB	NA
contig00111	943	2691	MSBA	0/0	100.0	99.9	MEG_4061	Drugs:Multi-drug_resistance:Multi-drug_ABC_efflux_pumps:MSBA	NA
contig00924	317	649	MVRC	0/0	100.0	92.2	MEG_4103	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MVRC	NA
contig00023	7786	8442	QNRS	0/0	100.0	100.0	MEG_6020	Drugs:Fluoroquinolones:Quinolone_resistance_protein_Qnr:QNRS	NA
contig00247	2358	3227	ROBA	0/0	100.0	99.0	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig01209	624	946	SOXS	0/0	99.7	99.7	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00120	1556	2371	SULII	0/0	100.0	100.0	MEG_6617	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULII	NA
contig00367	805	2050	TEM	0/0	98.3	99.4	MEG_6875	Drugs:betalactams:Class_A_betalactamases:TEM	NA
contig00470	1320	2594	TETA	0/0	100.0	100.0	MEG_7024	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETA	NA
contig00002	35344	36510	UGD	0/0	100.0	98.4	MEG_7328	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:UGD	NA

ID049

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00108	1505	2293	aadA5_1	0/0	100.0	100.0	AF137361	aadA5	Streptomycin
contig00131	938	1741	aph(3’’)-Ib_5	0/0	100.0	100.0	AF321551	aph(3’’)-Ib	Streptomycin
contig00131	102	938	aph(6)-Id_1	0/0	100.0	99.9	M28829	aph(6)-Id	Streptomycin
contig00125	429	1304	blaCTX-M-27_1	0/0	100.0	100.0	AY156923	blaCTX-M-27	Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig00108	901	1374	dfrA17_1	0/0	100.0	100.0	FJ460238	dfrA17	Trimethoprim
contig00016	44442	45674	mdf(A)_1	0/0	100.0	99.9	Y08743	mdf(A)
contig00166	69	897	mph(A)_1	0/0	91.5	100.0	D16251	mph(A)	Erythromycin, Azithromycin, Spiramycin, Telithromycin
contig00108	2813	3679	sul1_5	0/0	100.0	99.9	EU780013	sul1	Sulfamethoxazole
contig00131	1802	2617	sul2_2	0/0	100.0	100.0	AY034138	sul2	Sulfamethoxazole
contig00130	829	2075	tet(A)_6	0/0	97.8	100.0	AF534183	tet(A)	Doxycycline, Tetracycline

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00108	1505	2293	aadA5	0/0	100.0	100.0	AF137361:63-852	aadA5 is an aminoglycoside nucleotidyltransferase gene encoded by plasmids transposons and integrons in E. coli K. pneumoniae Kluyvera georgiana P. aeruginosa and E. cloacae	aminoglycoside
contig00008	69515	72664	acrB	0/0	100.0	100.0	U00096.3:484403-481253	Protein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug/proton antiporter.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00009	39212	42325	acrD	0/0	100.0	99.9	AP009048.1:2586250-2589364	AcrD is an aminoglycoside efflux pump expressed in E. coli. Its expression can be induced by indole and is regulated by baeRS and cpxAR.	aminoglycoside
contig00131	938	1741	APH(3’’)-Ib	0/0	100.0	99.8	AF313472:15593-16397	APH(3’’)-Ib is an aminoglycoside phosphotransferase encoded by plasmids transposons integrative conjugative elements and chromosomes in Enterobacteriaceae and Pseudomonas spp.	aminoglycoside
contig00131	102	938	APH(6)-Id	0/0	100.0	99.8	AF024602:3155-3992	APH(6)-Id is an aminoglycoside phosphotransferase encoded by plasmids integrative conjugative elements and chromosomal genomic islands in K. pneumoniae Salmonella spp. E. coli Shigella flexneri Providencia alcalifaciens Pseudomonas spp. V. cholerae Edwardsiella tarda Pasteurella multocida and Aeromonas bestiarum	aminoglycoside
contig00029	48202	49023	bacA	0/0	100.0	99.9	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00002	81627	82349	baeR	0/0	100.0	100.0	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00002	80227	81630	baeS	0/0	100.0	98.9	AP009048:2165012-2166416	BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.	aminocoumarin, aminoglycoside
contig00017	61323	62696	cpxA	0/0	100.0	99.0	BA000007.3:4905062-4903688	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	aminocoumarin, aminoglycoside
contig00057	15366	15998	CRP	0/0	100.0	99.4	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00125	429	1304	CTX-M-27	0/0	100.0	100.0	AY156923:0-876	CTX-M-27 is a beta-lactamase found in Escherichia coli	cephalosporin
contig00108	901	1374	dfrA17	0/0	100.0	100.0	DQ838665:0-474	dfrA17 is an integron-encoded dihydrofolate reductase found in Escherichia coli	diaminopyrimidine
contig00018	19811	20983	emrA	0/0	100.0	99.9	AP009048:2810082-2811255	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	fluoroquinolone
contig00018	21000	22538	emrB	0/0	100.0	99.9	U00096:2812615-2814154	emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin.	fluoroquinolone
contig00047	5171	6226	emrK	0/0	100.0	99.9	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00018	19154	19684	emrR	0/0	100.0	100.0	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00047	3633	5171	emrY	0/0	100.0	99.0	D78168:1591-3130	emrY is a multidrug transport that moves substrates across the inner membrane of the Gram-negative E. coli. It is a homolog of emrB.	tetracycline
contig00004	110892	112535	eptA	0/0	100.0	99.3	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00008	72687	73880	Escherichia_coli_acrA	0/0	100.0	100.0	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00020	17734	18867	Escherichia_coli_ampC	0/0	100.0	97.3	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00009	73700	75004	Escherichia_coli_ampC1_beta-lactamase	0/0	100.0	99.9	FN649414.1:2765050-2766355	An ampC-like beta-lactamase identified from Escherichia coli.	cephalosporin, penam
contig00073	15454	16611	Escherichia_coli_ampH	0/0	100.0	98.9	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig00001	133978	134310	Escherichia_coli_emrE	0/0	100.0	92.2	Z11877.1:485-818	Member of the small MDR (multidrug resistance) family of transporters, in Escherichia coli this protein provides resistance against a number of positively charged compounds including ethidium bromide and erythromycin, proton-dependent secondary transporter which exchanges protons for compound translocation	macrolide
contig00016	44442	45674	Escherichia_coli_mdfA	0/0	100.0	98.4	JQ394987:0-1233	Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter.	benzalkonium_chloride, rhodamine, tetracycline
contig00047	6750	7364	evgA	0/0	100.0	100.0	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00047	7369	10962	evgS	0/0	100.0	99.7	U00096:2484373-2487967	EvgS is a sensor protein that phosphorylates the regulatory protein EvgA. evgS corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	fluoroquinolone, macrolide, penam, tetracycline
contig00022	55847	56575	gadW	0/0	100.0	94.7	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig00022	54655	55479	gadX	0/0	100.0	99.9	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00058	21058	21471	H-NS	0/0	100.0	99.5	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00036	8068	8745	kdpE	0/0	100.0	100.0	U00096.3:721733-721055	kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding.	aminoglycoside
contig00082	14558	14941	marA	0/0	100.0	99.5	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00002	71367	72614	mdtA	0/0	100.0	100.0	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00002	72614	75736	mdtB	0/0	100.0	98.3	U00096:2155262-2158385	MdtB is a transporter that forms a heteromultimer complex with MdtC to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex.	aminocoumarin
contig00002	75737	78814	mdtC	0/0	100.0	97.7	U00096:2158385-2161463	MdtC is a transporter that forms a heteromultimer complex with MdtB to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex. In the absence of MdtB MdtC can form a homomultimer complex that results in a functioning efflux complex with a narrower drug specificity. mdtC corresponds to 3 loci in Pseudomonas aeruginosa PAO1 (gene name: muxC/muxB) and 3 loci in Pseudomonas aeruginosa LESB58.	aminocoumarin
contig00022	60076	61233	mdtE	0/0	100.0	100.0	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00022	56938	60051	mdtF	0/0	100.0	99.9	U00096:3660413-3663527	MdtF is the multidrug inner membrane transporter for the MdtEF-TolC efflux complex.	fluoroquinolone, macrolide, penam
contig00010	33212	34438	mdtG	0/0	100.0	99.3	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00010	43067	44275	mdtH	0/0	100.0	99.9	U00096:1125326-1124117	Multidrug resistance protein MdtH	fluoroquinolone
contig00034	261	1472	mdtM	0/0	98.3	95.5	U00096.3:4568519-4567286	Multidrug resistance protein MdtM	acridine_dye, fluoroquinolone, lincosamide, nucleoside, phenicol
contig00004	80031	81062	mdtN	0/0	100.0	100.0	AP009048.1:4307588-4306556	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	acridine_dye, nucleoside
contig00004	77980	80031	mdtO	0/0	100.0	99.8	AP009048.1:4306557-4304505	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00004	76517	77983	mdtP	0/0	100.0	100.0	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00166	69	897	mphA	0/0	91.5	100.0	D16251.1:2531-1625	The mphA gene encodes for resistance enzyme MPH(2’)-I which preferentially inactivate 14-membered macrolides (e.g.erythromycin telithromycin roxithromycin) over 16-membered macrolides (e.g.tylosin spiramycin). It phosphorylates macrolides at 2’-OH hydroxyl of desosamine sugar of macrolides in a GTP-dependent manner.	macrolide
contig00009	18219	18693	mphB	0/0	99.6	97.3	AE005174.2:3397370-3397847	The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides.	macrolide
contig00033	25708	27456	msbA	0/0	100.0	100.0	U00096.3:966620-968369	MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability.	nitroimidazole
contig00005	106683	107651	pmrF	0/0	100.0	100.0	U00096:2367070-2368039	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide
contig00108	2840	3679	sul1	0/0	100.0	100.0	JF969163:1053-1893	Sul1 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria. It is linked to other resistance genes of class 1 integrons.	sulfonamide
contig00131	1802	2617	sul2	0/0	100.0	100.0	AY055428.1:21084-20268	Sul2 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria usually found on small plasmids.	sulfonamide
contig00130	829	2075	tet(A)	0/0	97.8	100.0	AF534183.1:2970-4245	TetA is a tetracycline efflux pump found in many species of Gram-negative bacteria.	tetracycline
contig00054	19230	20717	tolC	0/0	100.0	99.7	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan
contig00002	20864	22030	ugd	0/0	100.0	96.2	U00096:2099613-2098446	PmrE is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin	peptide
contig00005	46584	48227	yojI	0/0	100.0	100.0	U00096.3:2308615-2306971	YojI mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. YojI is capable of pumping out microcin molecules. The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI.	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00108	1505	2293	(AGly)aadA5	0/0	100.0	100.0	AF137361:64-852	(AGly)aadA5	NA
contig00131	938	1741	(AGly)strA	0/0	100.0	99.9	AB366441:22458-23261	(AGly)strA	NA
contig00131	102	938	(AGly)strB	0/0	100.0	99.9	FJ474091:264-1100	(AGly)strB	NA
contig00009	73700	75004	(Bla)AmpC1_Ecoli	0/0	100.0	99.9	FN649414:2765051-2766355	(Bla)AmpC1_Ecoli	NA
contig00020	17734	18867	(Bla)AmpC2_Ecoli	0/0	100.0	97.3	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00073	15454	16611	(Bla)ampH_Ecoli	0/0	100.0	98.9	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00125	429	1304	(Bla)blaCTX-M-27	0/0	100.0	100.0	AY156923:1-876	(Bla)blaCTX-M-27	NA
contig00024	8297	10198	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100.0	100.0	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA
contig00166	69	897	(MLS)mph(A)	0/0	91.5	100.0	DQ445270:1626-2531	(MLS)mph(A)	NA
contig00108	2840	3679	(Sul)sul1	0/0	100.0	100.0	AF071413:6700-7539	(Sul)sul1	NA
contig00131	1802	2617	(Sul)sul2	0/0	100.0	100.0	EU360945:1617-2432	(Sul)sul2	NA
contig00130	829	2103	(Tet)tetA	0/0	100.0	100.0	JX424423:94438-95712	(Tet)tetA	NA
contig00130	172	798	(Tet)tetR	1/24	96.3	96.3	HF545434:53576-54226	(Tet)tetR	NA
contig00108	901	1374	(Tmt)dfrA17	0/0	100.0	100.0	AB126604:98-571	(Tmt)dfrA17	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00108	1505	2293	aadA5	0/0	100.0	100.0	NG_047357.1	ANT(3’’)-Ia family aminoglycoside nucleotidyltransferase AadA5	STREPTOMYCIN
contig00131	938	1765	aph(3’’)-Ib	0/0	100.0	100.0	NG_056002.2	aminoglycoside O-phosphotransferase APH(3’’)-Ib	STREPTOMYCIN
contig00131	102	938	aph(6)-Id	0/0	100.0	100.0	NG_047466.1	aminoglycoside O-phosphotransferase APH(6)-Id	STREPTOMYCIN
contig00125	429	1304	blaCTX-M-27	0/0	100.0	100.0	NG_048976.1	class A extended-spectrum beta-lactamase CTX-M-27	CEPHALOSPORIN
contig00020	17734	18867	blaEC-15	0/0	100.0	98.6	NG_049081.1	class C extended-spectrum beta-lactamase EC-15	CEPHALOSPORIN
contig00108	901	1374	dfrA17	0/0	100.0	99.8	NG_047710.1	trimethoprim-resistant dihydrofolate reductase DfrA17	TRIMETHOPRIM
contig00166	69	897	mph(A)	0/0	91.5	100.0	NG_047985.1	Mph(A) family macrolide 2’-phosphotransferase	MACROLIDE
contig00108	2840	3679	sul1	0/0	100.0	100.0	NG_048082.1	sulfonamide-resistant dihydropteroate synthase Sul1	SULFONAMIDE
contig00131	1802	2617	sul2	0/0	100.0	100.0	NG_051852.1	sulfonamide-resistant dihydropteroate synthase Sul2	SULFONAMIDE
contig00130	904	2103	tet(A)	0/0	100.0	100.0	NG_048154.1	tetracycline efflux MFS transporter Tet(A)	TETRACYCLINE

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00008	72687	73880	ACRA	0/0	100.0	100.0	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00008	69515	72664	ACRB	0/0	100.0	100.0	MEG_401	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRB	NA
contig00009	39212	42325	ACRD	0/0	100.0	99.9	MEG_407	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ACRD	NA
contig00073	15454	16611	AMPH	0/0	100.0	98.9	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00108	1505	2293	ANT3-DPRIME	0/0	100.0	100.0	MEG_928	Drugs:Aminoglycosides:Aminoglycoside_O-nucleotidyltransferases:ANT3-DPRIME	NA
contig00131	938	1765	APH3-DPRIME	0/0	100.0	100.0	MEG_1019	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH3-DPRIME	NA
contig00131	102	938	APH6	0/0	100.0	100.0	MEG_1084	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH6	NA
contig00002	57111	58963	ASMA	0/0	100.0	93.9	MEG_1180	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:ASMA	NA
contig00029	48202	49023	BACA	0/0	100.0	99.9	MEG_1190	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00002	81627	82349	BAER	0/0	100.0	100.0	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00002	80227	81630	BAES	0/0	100.0	98.9	MEG_1193	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES	NA
contig00005	19496	20686	BCR	0/0	100.0	100.0	MEG_1210	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR	NA
contig00020	17734	18867	BLAEC	0/0	100.0	98.6	MEG_1282	Drugs:betalactams:Class_C_betalactamases:BLAEC	NA
contig00017	60628	61326	CPXAR	0/0	100.0	100.0	MEG_2122	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00017	61323	62696	CPXAR	0/0	100.0	100.0	MEG_2121	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00057	15366	15998	CRP	0/0	100.0	99.4	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00125	407	1310	CTX	0/0	100.0	99.8	MEG_2401	Drugs:betalactams:Class_A_betalactamases:CTX	NA
contig00125	1339	2281	CTX	0/0	100.0	100.0	MEG_2435	Drugs:betalactams:Class_A_betalactamases:CTX	NA
contig00108	901	1374	DFRA	0/0	100.0	100.0	MEG_2547	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00018	19811	20983	EMRA	0/0	100.0	99.9	MEG_2722	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA	NA
contig00018	21000	22538	EMRB	0/0	100.0	99.9	MEG_2725	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRB	NA
contig00069	19743	20933	EMRD	0/0	100.0	99.9	MEG_2729	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD	NA
contig00047	5171	6334	EMRK	0/0	100.0	99.9	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig00018	19154	19684	EMRR	0/0	100.0	100.0	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00047	3633	5171	EMRY	0/0	100.0	99.0	MEG_2736	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRY	NA
contig00004	110892	112535	EPTA	0/0	100.0	99.3	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig00047	7369	10962	EVGS	0/0	100.0	99.7	MEG_2870	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EVGS	NA
contig00022	55847	56575	GADW	0/0	100.0	100.0	MEG_3081	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig00022	54655	55479	GADX	0/0	100.0	99.9	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00058	21058	21471	HNS	0/0	100.0	99.5	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00036	8068	8745	KDPE	0/0	100.0	100.0	MEG_3448	Drugs:Aminoglycosides:Aminoglycoside_efflux_pumps:KDPE	NA
contig00082	14552	14941	MARA	0/0	100.0	99.5	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00082	14103	14537	MARR	0/0	100.0	98.4	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00016	44442	45674	MDFA	0/0	100.0	100.0	MEG_3737	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDFA	NA
contig00002	71367	72614	MDTA	0/0	100.0	100.0	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00002	72614	75736	MDTB	0/0	100.0	98.3	MEG_3747	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTB	NA
contig00002	75737	78814	MDTC	0/0	100.0	97.7	MEG_3749	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTC	NA
contig00022	60076	61233	MDTE	0/0	100.0	100.0	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00022	56938	60051	MDTF	0/0	100.0	99.9	MEG_3752	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTF	NA
contig00010	33212	34438	MDTG	0/0	100.0	99.8	MEG_3753	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig00010	43067	44275	MDTH	0/0	100.0	99.9	MEG_3755	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTH	NA
contig00135	852	1181	MDTI	0/0	100.0	100.0	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00135	500	865	MDTJ	0/0	100.0	99.5	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00027	27080	28453	MDTK	0/0	100.0	100.0	MEG_3759	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:MDTK	NA
contig00034	261	1472	MDTM	0/0	98.3	95.5	MEG_3761	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTM	NA
contig00004	80031	81062	MDTN	0/0	100.0	100.0	MEG_3763	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN	NA
contig00004	77980	80031	MDTO	0/0	100.0	99.8	MEG_3764	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTO	NA
contig00004	76517	77983	MDTP	0/0	100.0	100.0	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig00166	69	897	MPHA	0/0	91.5	100.0	MEG_4029	Drugs:MLS:Macrolide_phosphotransferases:MPHA	NA
contig00009	18219	18693	MPHB	0/0	99.6	97.3	MEG_4033	Drugs:MLS:Macrolide_phosphotransferases:MPHB	NA
contig00033	25708	27456	MSBA	0/0	100.0	100.0	MEG_4061	Drugs:Multi-drug_resistance:Multi-drug_ABC_efflux_pumps:MSBA	NA
contig00001	133978	134310	MVRC	0/0	100.0	92.2	MEG_4103	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MVRC	NA
contig00024	8297	10198	PBP2	0/0	100.0	100.0	MEG_5400	Drugs:betalactams:Penicillin_binding_protein:PBP2	NA
contig00009	73700	75004	PBP4B	0/0	100.0	99.9	MEG_5409	Drugs:betalactams:Penicillin_binding_protein:PBP4B	NA
contig00005	106683	107651	PMRF	0/0	100.0	100.0	MEG_5801	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF	NA
contig00021	21724	22593	ROBA	0/0	100.0	98.8	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00004	54319	54641	SOXS	0/0	99.7	99.7	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00108	2839	3806	SULI	0/0	100.0	100.0	MEG_6615	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULI	NA
contig00131	1802	2617	SULII	0/0	100.0	100.0	MEG_6617	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULII	NA
contig00130	829	2103	TETA	0/0	100.0	100.0	MEG_7024	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETA	NA
contig00002	20864	22030	UGD	0/0	100.0	96.2	MEG_7328	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:UGD	NA
contig00005	46584	48227	YOGI	0/0	100.0	100.0	MEG_7842	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:YOGI	NA

ID051

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00066	1696	2556	aac(3)-IIa_1	0/0	100.0	99.8	X51534	aac(3)-IIa	Gentamicin, Tobramycin
contig00049	1638	2426	aadA5_1	0/0	100.0	100.0	AF137361	aadA5	Streptomycin
contig00063	971	1774	aph(3’’)-Ib_5	0/0	100.0	100.0	AF321551	aph(3’’)-Ib	Streptomycin
contig00063	135	971	aph(6)-Id_1	0/0	100.0	99.9	M28829	aph(6)-Id	Streptomycin
contig00052	2407	3282	blaCTX-M-15_1	0/0	100.0	100.0	AY044436	blaCTX-M-15	Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig00049	1034	1507	dfrA17_1	0/0	100.0	100.0	FJ460238	dfrA17	Trimethoprim
contig00002	29926	31158	mdf(A)_1	0/0	100.0	97.8	Y08743	mdf(A)
contig00080	69	967	mph(A)_1	0/0	99.2	100.0	D16251	mph(A)	Erythromycin, Azithromycin, Spiramycin, Telithromycin
contig00049	2946	3812	sul1_5	0/0	100.0	99.9	EU780013	sul1	Sulfamethoxazole
contig00063	1835	2650	sul2_2	0/0	100.0	100.0	AY034138	sul2	Sulfamethoxazole
contig00062	1435	2681	tet(A)_6	0/0	97.8	100.0	AF534183	tet(A)	Doxycycline, Tetracycline

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00066	1696	2556	AAC(3)-IIe	0/0	100.0	99.5	EU022315.1:0-861	AAC(3)-IIe is a plasmid-encoded aminoglycoside acetyltransferase in E. coli	aminoglycoside
contig00049	1638	2426	aadA5	0/0	100.0	100.0	AF137361:63-852	aadA5 is an aminoglycoside nucleotidyltransferase gene encoded by plasmids transposons and integrons in E. coli K. pneumoniae Kluyvera georgiana P. aeruginosa and E. cloacae	aminoglycoside
contig00006	65994	69143	acrB	0/0	100.0	98.8	U00096.3:484403-481253	Protein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug/proton antiporter.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00007	99473	102586	acrD	0/0	100.0	98.7	AP009048.1:2586250-2589364	AcrD is an aminoglycoside efflux pump expressed in E. coli. Its expression can be induced by indole and is regulated by baeRS and cpxAR.	aminoglycoside
contig00012	149301	150458	acrE	0/0	100.0	98.8	U00096:3413863-3415021	AcrE is a membrane fusion protein similar to AcrA.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00012	150470	153574	acrF	0/0	100.0	96.6	U00096:3415032-3418137	AcrF is a inner membrane transporter similar to AcrB.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00012	148240	148902	acrS	0/0	100.0	98.3	U00096:3413465-3412802	AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.	cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00063	971	1774	APH(3’’)-Ib	0/0	100.0	99.8	AF313472:15593-16397	APH(3’’)-Ib is an aminoglycoside phosphotransferase encoded by plasmids transposons integrative conjugative elements and chromosomes in Enterobacteriaceae and Pseudomonas spp.	aminoglycoside
contig00063	135	971	APH(6)-Id	0/0	100.0	99.8	AF024602:3155-3992	APH(6)-Id is an aminoglycoside phosphotransferase encoded by plasmids integrative conjugative elements and chromosomal genomic islands in K. pneumoniae Salmonella spp. E. coli Shigella flexneri Providencia alcalifaciens Pseudomonas spp. V. cholerae Edwardsiella tarda Pasteurella multocida and Aeromonas bestiarum	aminoglycoside
contig00008	52237	53056	bacA	0/0	99.8	98.3	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00001	336758	337479	baeR	0/0	99.9	97.1	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00001	337476	338879	baeS	0/0	100.0	90.5	AP009048:2165012-2166416	BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.	aminocoumarin, aminoglycoside
contig00018	66576	67943	cpxA	0/0	99.6	98.5	BA000007.3:4905062-4903688	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	aminocoumarin, aminoglycoside
contig00013	15089	15721	CRP	0/0	100.0	99.2	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00052	2407	3282	CTX-M-15	0/0	100.0	100.0	AY044436:1435-2311	CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family	cephalosporin
contig00049	1034	1507	dfrA17	0/0	100.0	100.0	DQ838665:0-474	dfrA17 is an integron-encoded dihydrofolate reductase found in Escherichia coli	diaminopyrimidine
contig00025	60096	61268	emrA	0/0	100.0	98.0	AP009048:2810082-2811255	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	fluoroquinolone
contig00025	61285	62823	emrB	0/0	100.0	98.4	U00096:2812615-2814154	emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin.	fluoroquinolone
contig00007	5703	6758	emrK	0/0	100.0	97.7	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00025	59439	59969	emrR	0/0	100.0	98.5	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00007	4165	5703	emrY	0/0	100.0	97.7	D78168:1591-3130	emrY is a multidrug transport that moves substrates across the inner membrane of the Gram-negative E. coli. It is a homolog of emrB.	tetracycline
contig00010	146399	148042	eptA	0/0	100.0	91.4	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00006	64778	65971	Escherichia_coli_acrA	0/0	100.0	99.1	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00023	48073	49206	Escherichia_coli_ampC	0/0	100.0	97.8	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00006	153893	155050	Escherichia_coli_ampH	0/0	100.0	97.1	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig00015	28735	29067	Escherichia_coli_emrE	0/0	100.0	92.2	Z11877.1:485-818	Member of the small MDR (multidrug resistance) family of transporters, in Escherichia coli this protein provides resistance against a number of positively charged compounds including ethidium bromide and erythromycin, proton-dependent secondary transporter which exchanges protons for compound translocation	macrolide
contig00002	29926	31158	Escherichia_coli_mdfA	0/0	100.0	96.3	JQ394987:0-1233	Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter.	benzalkonium_chloride, rhodamine, tetracycline
contig00007	7282	7896	evgA	0/0	100.0	99.0	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00007	7901	11494	evgS	0/0	100.0	96.3	U00096:2484373-2487967	EvgS is a sensor protein that phosphorylates the regulatory protein EvgA. evgS corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	fluoroquinolone, macrolide, penam, tetracycline
contig00028	1556	2284	gadW	0/0	100.0	100.0	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig00028	363	1187	gadX	0/0	100.0	93.9	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00021	63976	64389	H-NS	0/0	100.0	99.3	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00002	185279	185951	kdpE	0/0	99.3	95.5	U00096.3:721733-721055	kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding.	aminoglycoside
contig00004	289457	289840	marA	0/0	100.0	99.0	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00001	346492	347739	mdtA	0/0	100.0	95.6	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00001	343370	346492	mdtB	0/0	100.0	96.2	U00096:2155262-2158385	MdtB is a transporter that forms a heteromultimer complex with MdtC to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex.	aminocoumarin
contig00001	340292	343369	mdtC	0/0	100.0	94.0	U00096:2158385-2161463	MdtC is a transporter that forms a heteromultimer complex with MdtB to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex. In the absence of MdtB MdtC can form a homomultimer complex that results in a functioning efflux complex with a narrower drug specificity. mdtC corresponds to 3 loci in Pseudomonas aeruginosa PAO1 (gene name: muxC/muxB) and 3 loci in Pseudomonas aeruginosa LESB58.	aminocoumarin
contig00028	5785	6942	mdtE	0/0	100.0	98.5	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00028	2647	5760	mdtF	0/0	100.0	97.3	U00096:3660413-3663527	MdtF is the multidrug inner membrane transporter for the MdtEF-TolC efflux complex.	fluoroquinolone, macrolide, penam
contig00009	122719	123945	mdtG	0/0	100.0	98.4	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00009	112882	114090	mdtH	0/0	100.0	98.3	U00096:1125326-1124117	Multidrug resistance protein MdtH	fluoroquinolone
contig00003	306754	307986	mdtM	0/0	100.0	95.0	U00096.3:4568519-4567286	Multidrug resistance protein MdtM	acridine_dye, fluoroquinolone, lincosamide, nucleoside, phenicol
contig00010	116126	117157	mdtN	0/0	100.0	96.2	AP009048.1:4307588-4306556	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	acridine_dye, nucleoside
contig00010	114075	116126	mdtO	0/0	100.0	97.0	AP009048.1:4306557-4304505	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00010	112612	114078	mdtP	0/0	100.0	97.6	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00080	69	967	mphA	0/0	99.2	100.0	D16251.1:2531-1625	The mphA gene encodes for resistance enzyme MPH(2’)-I which preferentially inactivate 14-membered macrolides (e.g.erythromycin telithromycin roxithromycin) over 16-membered macrolides (e.g.tylosin spiramycin). It phosphorylates macrolides at 2’-OH hydroxyl of desosamine sugar of macrolides in a GTP-dependent manner.	macrolide
contig00017	45415	47163	msbA	0/0	100.0	98.1	U00096.3:966620-968369	MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability.	nitroimidazole
contig00001	102753	103721	pmrF	0/0	100.0	97.6	U00096:2367070-2368039	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide
contig00049	2973	3812	sul1	0/0	100.0	100.0	JF969163:1053-1893	Sul1 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria. It is linked to other resistance genes of class 1 integrons.	sulfonamide
contig00063	1835	2650	sul2	0/0	100.0	100.0	AY055428.1:21084-20268	Sul2 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria usually found on small plasmids.	sulfonamide
contig00062	1435	2681	tet(A)	0/0	97.8	100.0	AF534183.1:2970-4245	TetA is a tetracycline efflux pump found in many species of Gram-negative bacteria.	tetracycline
contig00008	78739	80226	tolC	0/0	100.0	98.2	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan
contig00001	400835	402001	ugd	0/0	100.0	96.0	U00096:2099613-2098446	PmrE is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin	peptide
contig00001	161926	163569	yojI	0/0	100.0	97.4	U00096.3:2308615-2306971	YojI mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. YojI is capable of pumping out microcin molecules. The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI.	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00066	1696	2556	(AGly)aac3-IIa	0/0	100.0	99.8	X51534:91-951	(AGly)aac3-IIa	NA
contig00049	1638	2426	(AGly)aadA5	0/0	100.0	100.0	AF137361:64-852	(AGly)aadA5	NA
contig00063	971	1774	(AGly)strA	0/0	100.0	99.9	AB366441:22458-23261	(AGly)strA	NA
contig00063	135	971	(AGly)strB	0/0	100.0	99.9	FJ474091:264-1100	(AGly)strB	NA
contig00023	48073	49206	(Bla)AmpC2_Ecoli	0/0	100.0	97.8	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00006	153893	155050	(Bla)ampH_Ecoli	0/0	100.0	97.1	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00052	2407	3282	(Bla)blaCTX-M-15	0/0	100.0	100.0	JQ686199:261-1136	(Bla)blaCTX-M-15	NA
contig00002	244497	246398	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100.0	98.7	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA
contig00080	69	967	(MLS)mph(A)	0/0	99.2	100.0	DQ445270:1626-2531	(MLS)mph(A)	NA
contig00049	2973	3812	(Sul)sul1	0/0	100.0	100.0	AF071413:6700-7539	(Sul)sul1	NA
contig00063	1835	2650	(Sul)sul2	0/0	100.0	100.0	EU360945:1617-2432	(Sul)sul2	NA
contig00062	1407	2681	(Tet)tetA	0/0	100.0	100.0	JX424423:94438-95712	(Tet)tetA	NA
contig00049	1034	1507	(Tmt)dfrA17	0/0	100.0	100.0	AB126604:98-571	(Tmt)dfrA17	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00066	1696	2556	aac(3)-IIe	0/0	100.0	99.8	NG_047244.1	aminoglycoside N-acetyltransferase AAC(3)-IIe	GENTAMICIN
contig00049	1638	2426	aadA5	0/0	100.0	100.0	NG_047357.1	ANT(3’’)-Ia family aminoglycoside nucleotidyltransferase AadA5	STREPTOMYCIN
contig00063	971	1798	aph(3’’)-Ib	0/0	100.0	100.0	NG_056002.2	aminoglycoside O-phosphotransferase APH(3’’)-Ib	STREPTOMYCIN
contig00063	135	971	aph(6)-Id	0/0	100.0	100.0	NG_047466.1	aminoglycoside O-phosphotransferase APH(6)-Id	STREPTOMYCIN
contig00052	2407	3282	blaCTX-M-15	0/0	100.0	100.0	NG_048935.1	class A extended-spectrum beta-lactamase CTX-M-15	CEPHALOSPORIN
contig00023	48073	49206	blaEC-5	0/0	100.0	99.5	NG_049085.1	cephalosporin-hydrolyzing class C beta-lactamase EC-5	CEPHALOSPORIN
contig00049	1034	1507	dfrA17	0/0	100.0	99.8	NG_047710.1	trimethoprim-resistant dihydrofolate reductase DfrA17	TRIMETHOPRIM
contig00080	69	967	mph(A)	0/0	99.2	100.0	NG_047985.1	Mph(A) family macrolide 2’-phosphotransferase	MACROLIDE
contig00049	2973	3812	sul1	0/0	100.0	100.0	NG_048082.1	sulfonamide-resistant dihydropteroate synthase Sul1	SULFONAMIDE
contig00063	1835	2650	sul2	0/0	100.0	100.0	NG_051852.1	sulfonamide-resistant dihydropteroate synthase Sul2	SULFONAMIDE
contig00062	1407	2606	tet(A)	0/0	100.0	100.0	NG_048154.1	tetracycline efflux MFS transporter Tet(A)	TETRACYCLINE

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00066	1696	2556	AAC3	0/0	100.0	99.8	MEG_44	Drugs:Aminoglycosides:Aminoglycoside_N-acetyltransferases:AAC3	NA
contig00006	64778	65971	ACRA	0/0	100.0	99.1	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00006	65994	69143	ACRB	0/0	100.0	98.8	MEG_401	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRB	NA
contig00007	99473	102586	ACRD	0/0	100.0	98.7	MEG_407	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ACRD	NA
contig00012	149301	150458	ACRE	0/0	100.0	98.8	MEG_408	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRE	NA
contig00012	150470	153574	ACRF	0/0	100.0	96.6	MEG_409	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRF	NA
contig00012	148240	148902	ACRS	0/0	100.0	98.3	MEG_415	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS	NA
contig00006	153893	155050	AMPH	0/0	100.0	97.1	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00049	1638	2426	ANT3-DPRIME	0/0	100.0	100.0	MEG_928	Drugs:Aminoglycosides:Aminoglycoside_O-nucleotidyltransferases:ANT3-DPRIME	NA
contig00063	971	1798	APH3-DPRIME	0/0	100.0	100.0	MEG_1019	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH3-DPRIME	NA
contig00063	135	971	APH6	0/0	100.0	100.0	MEG_1084	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH6	NA
contig00001	359399	361251	ASMA	0/0	100.0	97.6	MEG_1180	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:ASMA	NA
contig00008	52237	53056	BACA	0/0	99.8	98.5	MEG_1189	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00001	336758	337479	BAER	0/0	99.9	97.1	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00001	337476	338879	BAES	0/0	100.0	90.5	MEG_1193	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES	NA
contig00001	187202	188392	BCR	0/0	100.0	96.6	MEG_1210	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR	NA
contig00023	48073	49206	BLAEC	0/0	100.0	99.5	MEG_1275	Drugs:betalactams:Class_C_betalactamases:BLAEC	NA
contig00018	65881	66579	CPXAR	0/0	100.0	98.0	MEG_2118	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00018	66576	67943	CPXAR	0/0	99.6	99.0	MEG_2121	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00013	15089	15721	CRP	0/0	100.0	99.2	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00049	1034	1507	DFRA	0/0	100.0	100.0	MEG_2547	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00025	60096	61268	EMRA	0/0	100.0	98.0	MEG_2722	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA	NA
contig00025	61285	62823	EMRB	0/0	100.0	98.4	MEG_2725	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRB	NA
contig00005	194231	195421	EMRD	0/0	100.0	97.5	MEG_2729	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD	NA
contig00007	5703	6866	EMRK	0/0	100.0	97.4	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig00025	59439	59969	EMRR	0/0	100.0	98.5	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00007	4165	5703	EMRY	0/0	100.0	97.7	MEG_2736	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRY	NA
contig00010	146399	148042	EPTA	0/0	100.0	91.4	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig00007	7901	11494	EVGS	0/0	100.0	97.4	MEG_2869	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EVGS	NA
contig00028	1556	2284	GADW	0/0	100.0	100.0	MEG_3082	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig00028	363	1187	GADX	0/0	100.0	93.9	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00021	63976	64389	HNS	0/0	100.0	99.3	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00002	185279	185951	KDPE	0/0	99.3	95.5	MEG_3448	Drugs:Aminoglycosides:Aminoglycoside_efflux_pumps:KDPE	NA
contig00004	289457	289846	MARA	0/0	100.0	99.0	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00004	289861	290295	MARR	0/0	100.0	98.2	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00002	29926	31158	MDFA	0/0	100.0	97.9	MEG_3737	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDFA	NA
contig00001	346492	347739	MDTA	0/0	100.0	95.6	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00001	343370	346492	MDTB	0/0	100.0	96.2	MEG_3747	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTB	NA
contig00001	340292	343369	MDTC	0/0	100.0	94.0	MEG_3749	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTC	NA
contig00028	5785	6942	MDTE	0/0	100.0	98.5	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00028	2647	5760	MDTF	0/0	100.0	97.3	MEG_3752	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTF	NA
contig00009	122719	123945	MDTG	0/0	100.0	98.5	MEG_3753	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig00009	112882	114090	MDTH	0/0	100.0	98.3	MEG_3755	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTH	NA
contig00004	258563	258892	MDTI	0/0	100.0	98.8	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00004	258211	258576	MDTJ	0/0	100.0	98.4	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00004	191249	192621	MDTK	0/0	99.9	97.7	MEG_3759	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:MDTK	NA
contig00003	306754	307986	MDTM	0/0	100.0	95.0	MEG_3761	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTM	NA
contig00010	116126	117157	MDTN	0/0	100.0	96.2	MEG_3763	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN	NA
contig00010	114075	116126	MDTO	0/0	100.0	97.0	MEG_3764	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTO	NA
contig00010	112612	114078	MDTP	0/0	100.0	97.6	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig00080	69	967	MPHA	0/0	99.2	100.0	MEG_4029	Drugs:MLS:Macrolide_phosphotransferases:MPHA	NA
contig00017	45415	47163	MSBA	0/0	100.0	98.1	MEG_4061	Drugs:Multi-drug_resistance:Multi-drug_ABC_efflux_pumps:MSBA	NA
contig00015	28735	29067	MVRC	0/0	100.0	92.2	MEG_4103	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MVRC	NA
contig00002	244497	246398	PBP2	0/0	100.0	98.7	MEG_5400	Drugs:betalactams:Penicillin_binding_protein:PBP2	NA
contig00001	102753	103721	PMRF	0/0	100.0	97.6	MEG_5801	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF	NA
contig00003	247278	248147	ROBA	0/0	100.0	99.0	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00010	84259	84581	SOXS	0/0	99.7	98.1	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00049	2972	3939	SULI	0/0	100.0	100.0	MEG_6615	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULI	NA
contig00063	1835	2650	SULII	0/0	100.0	100.0	MEG_6617	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULII	NA
contig00062	1407	2681	TETA	0/0	100.0	100.0	MEG_7024	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETA	NA
contig00001	400835	402001	UGD	0/0	100.0	96.0	MEG_7328	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:UGD	NA
contig00001	161926	163569	YOGI	0/0	100.0	97.4	MEG_7842	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:YOGI	NA

ID054

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00038	23105	23908	aph(3’’)-Ib_5	0/0	100.0	100.0	AF321551	aph(3’’)-Ib	Streptomycin
contig00038	22269	23105	aph(6)-Id_1	0/0	100.0	100.0	M28829	aph(6)-Id	Streptomycin
contig00038	16991	17866	blaCTX-M-15_1	0/0	100.0	100.0	AY044436	blaCTX-M-15	Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig00038	20688	21548	blaTEM-1B_1	0/0	100.0	100.0	AY458016	blaTEM-1B	Amoxicillin, Ampicillin, Cephalothin, Piperacillin, Ticarcillin
contig00054	182	664	dfrA14_5	0/0	100.0	99.6	DQ388123	dfrA14	Trimethoprim
contig00021	64612	65844	mdf(A)_1	0/0	100.0	99.1	Y08743	mdf(A)
contig00038	11694	12350	qnrS1_1	0/0	100.0	100.0	AB187515	qnrS1	Ciprofloxacin
contig00038	23969	24784	sul2_2	0/0	100.0	100.0	AY034138	sul2	Sulfamethoxazole
contig00046	1676	2922	tet(A)_6	0/0	97.8	100.0	AF534183	tet(A)	Doxycycline, Tetracycline

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00010	124682	127831	acrB	0/0	100.0	99.1	U00096.3:484403-481253	Protein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug/proton antiporter.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00011	117709	120822	acrD	0/0	100.0	98.8	AP009048.1:2586250-2589364	AcrD is an aminoglycoside efflux pump expressed in E. coli. Its expression can be induced by indole and is regulated by baeRS and cpxAR.	aminoglycoside
contig00003	270324	271481	acrE	0/0	100.0	98.9	U00096:3413863-3415021	AcrE is a membrane fusion protein similar to AcrA.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00003	271493	274597	acrF	0/0	100.0	99.0	U00096:3415032-3418137	AcrF is a inner membrane transporter similar to AcrB.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00003	269263	269925	acrS	0/0	100.0	98.6	U00096:3413465-3412802	AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.	cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00038	23105	23908	APH(3’’)-Ib	0/0	100.0	99.8	AF313472:15593-16397	APH(3’’)-Ib is an aminoglycoside phosphotransferase encoded by plasmids transposons integrative conjugative elements and chromosomes in Enterobacteriaceae and Pseudomonas spp.	aminoglycoside
contig00038	22269	23105	APH(6)-Id	0/0	100.0	99.9	AF024602:3155-3992	APH(6)-Id is an aminoglycoside phosphotransferase encoded by plasmids integrative conjugative elements and chromosomal genomic islands in K. pneumoniae Salmonella spp. E. coli Shigella flexneri Providencia alcalifaciens Pseudomonas spp. V. cholerae Edwardsiella tarda Pasteurella multocida and Aeromonas bestiarum	aminoglycoside
contig00003	60020	60839	bacA	0/0	99.8	98.7	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00002	115445	116167	baeR	0/0	100.0	99.5	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00002	114045	115448	baeS	0/0	100.0	98.7	AP009048:2165012-2166416	BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.	aminocoumarin, aminoglycoside
contig00027	22853	24226	cpxA	0/0	100.0	98.5	BA000007.3:4905062-4903688	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	aminocoumarin, aminoglycoside
contig00007	15377	16009	CRP	0/0	100.0	99.2	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00038	16991	17866	CTX-M-15	0/0	100.0	100.0	AY044436:1435-2311	CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family	cephalosporin
contig00054	182	664	dfrA14	0/0	100.0	99.8	EU780012:2162-2645	dfrA14 is an integron-encoded dihydrofolate reductase found in Escherichia coli	diaminopyrimidine
contig00001	56948	58120	emrA	0/0	100.0	98.2	AP009048:2810082-2811255	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	fluoroquinolone
contig00001	58137	59675	emrB	0/0	100.0	98.5	U00096:2812615-2814154	emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin.	fluoroquinolone
contig00011	25955	27010	emrK	0/0	100.0	98.7	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00001	56291	56821	emrR	0/0	100.0	100.0	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00011	24417	25955	emrY	0/0	100.0	98.8	D78168:1591-3130	emrY is a multidrug transport that moves substrates across the inner membrane of the Gram-negative E. coli. It is a homolog of emrB.	tetracycline
contig00025	18397	20040	eptA	0/0	100.0	99.2	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00010	127854	129047	Escherichia_coli_acrA	0/0	100.0	99.8	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00016	92232	93365	Escherichia_coli_ampC	0/0	100.0	97.2	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00011	85287	86591	Escherichia_coli_ampC1_beta-lactamase	0/0	100.0	98.2	FN649414.1:2765050-2766355	An ampC-like beta-lactamase identified from Escherichia coli.	cephalosporin, penam
contig00010	36338	37495	Escherichia_coli_ampH	0/0	100.0	98.7	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig00029	3107	3439	Escherichia_coli_emrE	0/0	100.0	92.5	Z11877.1:485-818	Member of the small MDR (multidrug resistance) family of transporters, in Escherichia coli this protein provides resistance against a number of positively charged compounds including ethidium bromide and erythromycin, proton-dependent secondary transporter which exchanges protons for compound translocation	macrolide
contig00021	64612	65844	Escherichia_coli_mdfA	0/0	100.0	97.6	JQ394987:0-1233	Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter.	benzalkonium_chloride, rhodamine, tetracycline
contig00011	27534	28148	evgA	0/0	100.0	99.0	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00011	28153	31746	evgS	0/0	100.0	99.5	U00096:2484373-2487967	EvgS is a sensor protein that phosphorylates the regulatory protein EvgA. evgS corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	fluoroquinolone, macrolide, penam, tetracycline
contig00007	190423	191151	gadW	0/0	100.0	94.4	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig00007	191519	192343	gadX	0/0	100.0	97.8	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00004	201389	201802	H-NS	0/0	100.0	99.3	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00013	8305	8977	kdpE	0/0	99.3	97.2	U00096.3:721733-721055	kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding.	aminoglycoside
contig00024	52307	52690	marA	0/0	100.0	99.5	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00002	105185	106432	mdtA	0/0	100.0	98.2	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00002	106432	109554	mdtB	0/0	100.0	98.0	U00096:2155262-2158385	MdtB is a transporter that forms a heteromultimer complex with MdtC to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex.	aminocoumarin
contig00002	109555	112632	mdtC	0/0	100.0	98.1	U00096:2158385-2161463	MdtC is a transporter that forms a heteromultimer complex with MdtB to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex. In the absence of MdtB MdtC can form a homomultimer complex that results in a functioning efflux complex with a narrower drug specificity. mdtC corresponds to 3 loci in Pseudomonas aeruginosa PAO1 (gene name: muxC/muxB) and 3 loci in Pseudomonas aeruginosa LESB58.	aminocoumarin
contig00007	185765	186922	mdtE	0/0	100.0	99.7	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00007	186947	190060	mdtF	0/0	100.0	98.6	U00096:3660413-3663527	MdtF is the multidrug inner membrane transporter for the MdtEF-TolC efflux complex.	fluoroquinolone, macrolide, penam
contig00014	96840	98066	mdtG	0/0	100.0	99.2	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00014	87001	88209	mdtH	0/0	100.0	98.8	U00096:1125326-1124117	Multidrug resistance protein MdtH	fluoroquinolone
contig00015	82731	83963	mdtM	0/0	100.0	95.9	U00096.3:4568519-4567286	Multidrug resistance protein MdtM	acridine_dye, fluoroquinolone, lincosamide, nucleoside, phenicol
contig00017	4259	5290	mdtN	0/0	100.0	98.0	AP009048.1:4307588-4306556	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	acridine_dye, nucleoside
contig00017	5290	7341	mdtO	0/0	100.0	98.7	AP009048.1:4306557-4304505	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00017	7338	8804	mdtP	0/0	100.0	98.2	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00011	142312	142788	mphB	0/0	100.0	98.3	AE005174.2:3397370-3397847	The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides.	macrolide
contig00009	51625	53373	msbA	0/0	100.0	99.0	U00096.3:966620-968369	MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability.	nitroimidazole
contig00002	304508	305476	pmrF	0/0	100.0	99.4	U00096:2367070-2368039	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide
contig00038	11694	12350	QnrS1	0/0	100.0	100.0	DQ485529.1:0-657	QnrS1 is a plasmid-mediated quinolone resistance protein found in Shigella flexneri	fluoroquinolone
contig00038	23969	24784	sul2	0/0	100.0	100.0	AY055428.1:21084-20268	Sul2 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria usually found on small plasmids.	sulfonamide
contig00038	20688	21548	TEM-1	0/0	100.0	99.9	AL513383:161910-162771	TEM-1 is a broad-spectrum beta-lactamase found in many Gram-negative bacteria. Confers resistance to penicillins and first generation cephalosphorins.	cephalosporin, monobactam, penam, penem
contig00046	1676	2922	tet(A)	0/0	97.8	100.0	AF534183.1:2970-4245	TetA is a tetracycline efflux pump found in many species of Gram-negative bacteria.	tetracycline
contig00003	36175	37662	tolC	0/0	100.0	98.4	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan
contig00002	255847	257490	yojI	0/0	100.0	98.2	U00096.3:2308615-2306971	YojI mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. YojI is capable of pumping out microcin molecules. The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI.	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00038	23105	23908	(AGly)strA	0/0	100	99.9	AB366441:22458-23261	(AGly)strA	NA
contig00038	22269	23105	(AGly)strB	0/0	100	100.0	FJ474091:264-1100	(AGly)strB	NA
contig00011	85287	86591	(Bla)AmpC1_Ecoli	0/0	100	98.2	FN649414:2765051-2766355	(Bla)AmpC1_Ecoli	NA
contig00016	92232	93365	(Bla)AmpC2_Ecoli	0/0	100	97.2	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00010	36338	37495	(Bla)ampH_Ecoli	0/0	100	98.7	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00038	16991	17866	(Bla)blaCTX-M-15	0/0	100	100.0	JQ686199:261-1136	(Bla)blaCTX-M-15	NA
contig00038	20688	21548	(Bla)blaTEM-105	0/0	100	99.9	AF516720:215-1075	(Bla)blaTEM-105	NA
contig00013	60766	62667	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100	98.7	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA
contig00038	11694	12350	(Flq)qnr-S1	0/0	100	100.0	AB187515:9737-10393	(Flq)qnr-S1	NA
contig00038	23969	24784	(Sul)sul2	0/0	100	100.0	EU360945:1617-2432	(Sul)sul2	NA
contig00046	1648	2922	(Tet)tetA	0/0	100	100.0	JX424423:94438-95712	(Tet)tetA	NA
contig00054	182	655	(Tmt)dfrA14	0/0	100	100.0	GU726917:72-545	(Tmt)dfrA14	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00038	23105	23932	aph(3’’)-Ib	0/0	100	100.0	NG_056002.2	aminoglycoside O-phosphotransferase APH(3’’)-Ib	STREPTOMYCIN
contig00038	22269	23105	aph(6)-Id	0/0	100	100.0	NG_047464.1	aminoglycoside O-phosphotransferase APH(6)-Id	STREPTOMYCIN
contig00038	16991	17866	blaCTX-M-15	0/0	100	100.0	NG_048935.1	class A extended-spectrum beta-lactamase CTX-M-15	CEPHALOSPORIN
contig00016	92232	93365	blaEC-13	0/0	100	99.6	NG_049079.1	class C extended-spectrum beta-lactamase EC-13	CEPHALOSPORIN
contig00038	20688	21548	blaTEM-1	0/0	100	100.0	NG_050145.1	class A broad-spectrum beta-lactamase TEM-1	BETA-LACTAM
contig00054	182	655	dfrA14	0/0	100	100.0	NG_056035.1	trimethoprim-resistant dihydrofolate reductase DfrA14	TRIMETHOPRIM
contig00038	11694	12350	qnrS1	0/0	100	100.0	NG_050543.1	quinolone resistance pentapeptide repeat protein QnrS1	QUINOLONE
contig00038	23969	24784	sul2	0/0	100	100.0	NG_051852.1	sulfonamide-resistant dihydropteroate synthase Sul2	SULFONAMIDE
contig00046	1648	2847	tet(A)	0/0	100	100.0	NG_048154.1	tetracycline efflux MFS transporter Tet(A)	TETRACYCLINE

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00010	127854	129047	ACRA	0/0	100.0	99.8	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00010	124682	127831	ACRB	0/0	100.0	99.1	MEG_401	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRB	NA
contig00011	117709	120822	ACRD	0/0	100.0	98.8	MEG_407	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ACRD	NA
contig00003	270324	271481	ACRE	0/0	100.0	98.9	MEG_408	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRE	NA
contig00003	271493	274597	ACRF	0/0	100.0	99.0	MEG_409	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRF	NA
contig00003	269263	269925	ACRS	0/0	100.0	98.6	MEG_415	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS	NA
contig00010	36338	37495	AMPH	0/0	100.0	98.7	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00038	23105	23932	APH3-DPRIME	0/0	100.0	100.0	MEG_1019	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH3-DPRIME	NA
contig00038	22269	23105	APH6	0/0	100.0	100.0	MEG_1086	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH6	NA
contig00002	90930	92782	ASMA	0/0	100.0	98.0	MEG_1180	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:ASMA	NA
contig00003	60020	60839	BACA	0/0	99.8	98.9	MEG_1189	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00002	115445	116167	BAER	0/0	100.0	99.5	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00002	114045	115448	BAES	0/0	100.0	98.7	MEG_1193	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES	NA
contig00002	229386	230576	BCR	0/0	100.0	98.2	MEG_1210	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR	NA
contig00016	92232	93365	BLAEC	0/0	100.0	99.6	MEG_1280	Drugs:betalactams:Class_C_betalactamases:BLAEC	NA
contig00027	22158	22856	CPXAR	0/0	100.0	99.4	MEG_2118	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00027	22853	24226	CPXAR	0/0	100.0	99.1	MEG_2121	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00007	15377	16009	CRP	0/0	100.0	99.2	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00054	182	655	DFRA	0/0	100.0	99.8	MEG_2517	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00001	56948	58120	EMRA	0/0	100.0	98.2	MEG_2722	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA	NA
contig00001	58137	59675	EMRB	0/0	100.0	98.5	MEG_2725	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRB	NA
contig00008	92098	93288	EMRD	0/0	100.0	99.9	MEG_2729	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD	NA
contig00011	25955	27118	EMRK	0/0	100.0	98.8	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig00001	56291	56821	EMRR	0/0	100.0	100.0	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00011	24417	25955	EMRY	0/0	100.0	98.9	MEG_2736	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRY	NA
contig00025	18397	20040	EPTA	0/0	100.0	99.2	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig00011	28153	31746	EVGS	0/0	100.0	99.5	MEG_2870	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EVGS	NA
contig00007	190423	191151	GADW	0/0	100.0	98.6	MEG_3081	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig00007	191519	192343	GADX	0/0	100.0	97.8	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00004	201389	201802	HNS	0/0	100.0	99.3	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00013	8305	8977	KDPE	0/0	99.3	97.2	MEG_3448	Drugs:Aminoglycosides:Aminoglycoside_efflux_pumps:KDPE	NA
contig00024	52301	52690	MARA	0/0	100.0	99.5	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00024	51853	52287	MARR	0/0	100.0	97.7	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00021	64612	65844	MDFA	0/0	100.0	99.2	MEG_3737	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDFA	NA
contig00002	105185	106432	MDTA	0/0	100.0	98.2	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00002	106432	109554	MDTB	0/0	100.0	98.0	MEG_3747	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTB	NA
contig00002	109555	112632	MDTC	0/0	100.0	98.1	MEG_3749	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTC	NA
contig00007	185765	186922	MDTE	0/0	100.0	99.7	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00007	186947	190060	MDTF	0/0	100.0	98.6	MEG_3752	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTF	NA
contig00014	96840	98066	MDTG	0/0	100.0	99.3	MEG_3753	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig00014	87001	88209	MDTH	0/0	100.0	98.8	MEG_3755	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTH	NA
contig00005	206080	206409	MDTI	0/0	100.0	99.7	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00005	205728	206093	MDTJ	0/0	100.0	98.9	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00005	134590	135963	MDTK	0/0	100.0	99.0	MEG_3759	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:MDTK	NA
contig00015	82731	83963	MDTM	0/0	100.0	95.9	MEG_3761	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTM	NA
contig00017	4259	5290	MDTN	0/0	100.0	98.0	MEG_3763	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN	NA
contig00017	5290	7341	MDTO	0/0	100.0	98.7	MEG_3764	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTO	NA
contig00017	7338	8804	MDTP	0/0	100.0	98.2	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig00011	142312	142788	MPHB	0/0	100.0	98.3	MEG_4033	Drugs:MLS:Macrolide_phosphotransferases:MPHB	NA
contig00009	51625	53373	MSBA	0/0	100.0	99.0	MEG_4061	Drugs:Multi-drug_resistance:Multi-drug_ABC_efflux_pumps:MSBA	NA
contig00029	3107	3439	MVRC	0/0	100.0	92.5	MEG_4103	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MVRC	NA
contig00013	60766	62667	PBP2	0/0	100.0	98.7	MEG_5400	Drugs:betalactams:Penicillin_binding_protein:PBP2	NA
contig00011	85287	86591	PBP4B	0/0	100.0	98.2	MEG_5409	Drugs:betalactams:Penicillin_binding_protein:PBP4B	NA
contig00002	304508	305476	PMRF	0/0	100.0	99.4	MEG_5801	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF	NA
contig00038	11694	12350	QNRS	0/0	100.0	100.0	MEG_6020	Drugs:Fluoroquinolones:Quinolone_resistance_protein_Qnr:QNRS	NA
contig00015	11978	12847	ROBA	0/0	100.0	99.1	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00017	30421	30744	SOXS	0/0	100.0	100.0	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00038	23969	24784	SULII	0/0	100.0	100.0	MEG_6617	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULII	NA
contig00038	20321	21566	TEM	0/0	98.3	99.4	MEG_6875	Drugs:betalactams:Class_A_betalactamases:TEM	NA
contig00046	1648	2922	TETA	0/0	100.0	100.0	MEG_7024	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETA	NA
contig00002	255847	257490	YOGI	0/0	100.0	98.2	MEG_7842	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:YOGI	NA

ID057

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00064	2451	3239	aadA5_1	0/0	100.0	100.0	AF137361	aadA5	Streptomycin
contig00071	544	1419	blaCTX-M-15_1	0/0	100.0	100.0	AY044436	blaCTX-M-15	Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig00064	1847	2320	dfrA17_1	0/0	100.0	100.0	FJ460238	dfrA17	Trimethoprim
contig00003	33623	34855	mdf(A)_1	0/0	100.0	98.8	Y08743	mdf(A)
contig00092	68	989	mph(A)_2	1/1	100.0	99.7	U36578	mph(A)	Erythromycin, Azithromycin, Spiramycin, Telithromycin
contig00064	3759	4625	sul1_5	0/0	100.0	99.9	EU780013	sul1	Sulfamethoxazole
contig00077	1712	2958	tet(A)_6	0/0	97.8	100.0	AF534183	tet(A)	Doxycycline, Tetracycline

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00064	2451	3239	aadA5	0/0	100.0	100.0	AF137361:63-852	aadA5 is an aminoglycoside nucleotidyltransferase gene encoded by plasmids transposons and integrons in E. coli K. pneumoniae Kluyvera georgiana P. aeruginosa and E. cloacae	aminoglycoside
contig00006	89398	92547	acrB	0/0	100.0	99.1	U00096.3:484403-481253	Protein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug/proton antiporter.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00002	219081	222194	acrD	0/0	100.0	99.1	AP009048.1:2586250-2589364	AcrD is an aminoglycoside efflux pump expressed in E. coli. Its expression can be induced by indole and is regulated by baeRS and cpxAR.	aminoglycoside
contig00014	117852	119009	acrE	0/0	100.0	99.0	U00096:3413863-3415021	AcrE is a membrane fusion protein similar to AcrA.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00014	119021	122125	acrF	0/0	100.0	99.1	U00096:3415032-3418137	AcrF is a inner membrane transporter similar to AcrB.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00014	116791	117453	acrS	0/0	100.0	99.4	U00096:3413465-3412802	AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.	cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00001	226672	227493	bacA	0/0	100.0	98.7	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00007	122357	123079	baeR	0/0	100.0	99.5	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00007	123076	124479	baeS	0/0	100.0	98.1	AP009048:2165012-2166416	BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.	aminocoumarin, aminoglycoside
contig00043	22841	24214	cpxA	0/0	100.0	98.6	BA000007.3:4905062-4903688	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	aminocoumarin, aminoglycoside
contig00008	15366	15998	CRP	0/0	100.0	99.2	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00071	544	1419	CTX-M-15	0/0	100.0	100.0	AY044436:1435-2311	CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family	cephalosporin
contig00064	1847	2320	dfrA17	0/0	100.0	100.0	DQ838665:0-474	dfrA17 is an integron-encoded dihydrofolate reductase found in Escherichia coli	diaminopyrimidine
contig00037	5180	6352	emrA	0/0	100.0	97.5	AP009048:2810082-2811255	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	fluoroquinolone
contig00037	3625	5163	emrB	0/0	100.0	99.9	U00096:2812615-2814154	emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin.	fluoroquinolone
contig00002	123335	124390	emrK	0/0	100.0	99.7	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00037	6479	7009	emrR	0/0	100.0	100.0	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00002	121797	123335	emrY	0/0	100.0	99.7	D78168:1591-3130	emrY is a multidrug transport that moves substrates across the inner membrane of the Gram-negative E. coli. It is a homolog of emrB.	tetracycline
contig00028	18421	20064	eptA	0/0	100.0	99.3	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00006	92570	93763	Escherichia_coli_acrA	0/0	100.0	99.8	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00010	139346	140479	Escherichia_coli_ampC	0/0	100.0	97.3	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00002	186659	187963	Escherichia_coli_ampC1_beta-lactamase	0/0	100.0	98.6	FN649414.1:2765050-2766355	An ampC-like beta-lactamase identified from Escherichia coli.	cephalosporin, penam
contig00006	3378	4535	Escherichia_coli_ampH	0/0	100.0	99.4	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig00032	2794	3126	Escherichia_coli_emrE	0/0	100.0	91.9	Z11877.1:485-818	Member of the small MDR (multidrug resistance) family of transporters, in Escherichia coli this protein provides resistance against a number of positively charged compounds including ethidium bromide and erythromycin, proton-dependent secondary transporter which exchanges protons for compound translocation	macrolide
contig00003	33623	34855	Escherichia_coli_mdfA	0/0	100.0	97.2	JQ394987:0-1233	Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter.	benzalkonium_chloride, rhodamine, tetracycline
contig00002	124914	125528	evgA	0/0	100.0	99.0	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00002	125533	129126	evgS	0/0	100.0	99.4	U00096:2484373-2487967	EvgS is a sensor protein that phosphorylates the regulatory protein EvgA. evgS corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	fluoroquinolone, macrolide, penam, tetracycline
contig00039	2321	3049	gadW	0/0	100.0	94.4	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig00039	1129	1953	gadX	0/0	100.0	97.9	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00004	173073	173486	H-NS	0/0	100.0	99.5	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00017	8282	8954	kdpE	0/0	99.3	97.2	U00096.3:721733-721055	kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding.	aminoglycoside
contig00031	22703	23086	marA	0/0	100.0	99.5	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00007	132092	133339	mdtA	0/0	100.0	98.2	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00007	128970	132092	mdtB	0/0	100.0	99.8	U00096:2155262-2158385	MdtB is a transporter that forms a heteromultimer complex with MdtC to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex.	aminocoumarin
contig00007	125892	128969	mdtC	0/0	100.0	98.6	U00096:2158385-2161463	MdtC is a transporter that forms a heteromultimer complex with MdtB to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex. In the absence of MdtB MdtC can form a homomultimer complex that results in a functioning efflux complex with a narrower drug specificity. mdtC corresponds to 3 loci in Pseudomonas aeruginosa PAO1 (gene name: muxC/muxB) and 3 loci in Pseudomonas aeruginosa LESB58.	aminocoumarin
contig00039	6550	7707	mdtE	0/0	100.0	99.7	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00039	3412	6525	mdtF	0/0	100.0	98.4	U00096:3660413-3663527	MdtF is the multidrug inner membrane transporter for the MdtEF-TolC efflux complex.	fluoroquinolone, macrolide, penam
contig00015	86688	87914	mdtG	0/0	100.0	99.3	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00015	76849	78057	mdtH	0/0	100.0	98.4	U00096:1125326-1124117	Multidrug resistance protein MdtH	fluoroquinolone
contig00005	220370	221602	mdtM	0/0	100.0	96.3	U00096.3:4568519-4567286	Multidrug resistance protein MdtM	acridine_dye, fluoroquinolone, lincosamide, nucleoside, phenicol
contig00036	26171	27202	mdtN	0/0	100.0	98.1	AP009048.1:4307588-4306556	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	acridine_dye, nucleoside
contig00036	24120	26171	mdtO	0/0	100.0	98.4	AP009048.1:4306557-4304505	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00036	22657	24123	mdtP	0/0	100.0	98.2	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00092	68	973	mphA	0/0	100.0	100.0	D16251.1:2531-1625	The mphA gene encodes for resistance enzyme MPH(2’)-I which preferentially inactivate 14-membered macrolides (e.g.erythromycin telithromycin roxithromycin) over 16-membered macrolides (e.g.tylosin spiramycin). It phosphorylates macrolides at 2’-OH hydroxyl of desosamine sugar of macrolides in a GTP-dependent manner.	macrolide
contig00002	243431	243905	mphB	0/0	99.6	97.5	AE005174.2:3397370-3397847	The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides.	macrolide
contig00003	133636	135384	msbA	0/0	100.0	99.4	U00096.3:966620-968369	MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability.	nitroimidazole
contig00002	17662	18630	pmrF	0/0	100.0	99.3	U00096:2367070-2368039	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide
contig00064	3786	4625	sul1	0/0	100.0	100.0	JF969163:1053-1893	Sul1 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria. It is linked to other resistance genes of class 1 integrons.	sulfonamide
contig00077	1712	2958	tet(A)	0/0	97.8	100.0	AF534183.1:2970-4245	TetA is a tetracycline efflux pump found in many species of Gram-negative bacteria.	tetracycline
contig00001	202809	204296	tolC	0/0	100.0	99.7	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan
contig00024	42512	44155	yojI	0/0	100.0	98.1	U00096.3:2308615-2306971	YojI mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. YojI is capable of pumping out microcin molecules. The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI.	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00064	2451	3239	(AGly)aadA5	0/0	100	100.0	AF137361:64-852	(AGly)aadA5	NA
contig00002	186659	187963	(Bla)AmpC1_Ecoli	0/0	100	98.6	FN649414:2765051-2766355	(Bla)AmpC1_Ecoli	NA
contig00010	139346	140479	(Bla)AmpC2_Ecoli	0/0	100	97.3	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00006	3378	4535	(Bla)ampH_Ecoli	0/0	100	99.4	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00071	544	1419	(Bla)blaCTX-M-15	0/0	100	100.0	JQ686199:261-1136	(Bla)blaCTX-M-15	NA
contig00017	61082	62983	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100	99.0	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA
contig00092	68	973	(MLS)mph(A)	0/0	100	100.0	DQ445270:1626-2531	(MLS)mph(A)	NA
contig00064	3786	4625	(Sul)sul1	0/0	100	100.0	AF071413:6700-7539	(Sul)sul1	NA
contig00077	1684	2958	(Tet)tetA	0/0	100	100.0	JX424423:94438-95712	(Tet)tetA	NA
contig00064	1847	2320	(Tmt)dfrA17	0/0	100	100.0	AB126604:98-571	(Tmt)dfrA17	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00064	2451	3239	aadA5	0/0	100	100.0	NG_047357.1	ANT(3’’)-Ia family aminoglycoside nucleotidyltransferase AadA5	STREPTOMYCIN
contig00071	544	1419	blaCTX-M-15	0/0	100	100.0	NG_048935.1	class A extended-spectrum beta-lactamase CTX-M-15	CEPHALOSPORIN
contig00010	139346	140479	blaEC-15	0/0	100	98.6	NG_049081.1	class C extended-spectrum beta-lactamase EC-15	CEPHALOSPORIN
contig00064	1847	2320	dfrA17	0/0	100	99.8	NG_047710.1	trimethoprim-resistant dihydrofolate reductase DfrA17	TRIMETHOPRIM
contig00092	68	989	mph(A)	1/1	100	99.7	NG_047986.1	Mph(A) family macrolide 2’-phosphotransferase	MACROLIDE
contig00064	3786	4625	sul1	0/0	100	100.0	NG_048082.1	sulfonamide-resistant dihydropteroate synthase Sul1	SULFONAMIDE
contig00077	1684	2883	tet(A)	0/0	100	100.0	NG_048154.1	tetracycline efflux MFS transporter Tet(A)	TETRACYCLINE

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00006	92570	93763	ACRA	0/0	100.0	99.8	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00006	89398	92547	ACRB	0/0	100.0	99.1	MEG_401	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRB	NA
contig00002	219081	222194	ACRD	0/0	100.0	99.1	MEG_407	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ACRD	NA
contig00014	117852	119009	ACRE	0/0	100.0	99.0	MEG_408	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRE	NA
contig00014	119021	122125	ACRF	0/0	100.0	99.1	MEG_409	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRF	NA
contig00014	116791	117453	ACRS	0/0	100.0	99.4	MEG_415	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS	NA
contig00006	3378	4535	AMPH	0/0	100.0	99.4	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00064	2451	3239	ANT3-DPRIME	0/0	100.0	100.0	MEG_928	Drugs:Aminoglycosides:Aminoglycoside_O-nucleotidyltransferases:ANT3-DPRIME	NA
contig00007	146007	147859	ASMA	0/0	100.0	98.0	MEG_1180	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:ASMA	NA
contig00001	226672	227493	BACA	0/0	100.0	98.9	MEG_1189	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00007	122357	123079	BAER	0/0	100.0	99.5	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00007	123076	124479	BAES	0/0	100.0	98.1	MEG_1193	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES	NA
contig00007	8694	9884	BCR	0/0	100.0	96.6	MEG_1210	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR	NA
contig00010	139346	140479	BLAEC	0/0	100.0	98.6	MEG_1282	Drugs:betalactams:Class_C_betalactamases:BLAEC	NA
contig00043	22146	22844	CPXAR	0/0	100.0	99.1	MEG_2118	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00043	22841	24214	CPXAR	0/0	100.0	99.2	MEG_2121	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00008	15366	15998	CRP	0/0	100.0	99.2	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00064	1847	2320	DFRA	0/0	100.0	100.0	MEG_2547	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00037	5180	6352	EMRA	0/0	100.0	97.5	MEG_2722	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA	NA
contig00037	3625	5163	EMRB	0/0	100.0	99.9	MEG_2725	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRB	NA
contig00026	45787	46977	EMRD	0/0	100.0	99.9	MEG_2729	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD	NA
contig00002	123335	124498	EMRK	0/0	100.0	99.7	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig00037	6479	7009	EMRR	0/0	100.0	100.0	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00002	121797	123335	EMRY	0/0	100.0	99.7	MEG_2736	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRY	NA
contig00028	18421	20064	EPTA	0/0	100.0	99.3	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig00002	125533	129126	EVGS	0/0	100.0	99.4	MEG_2870	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EVGS	NA
contig00039	2321	3049	GADW	0/0	100.0	98.6	MEG_3081	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig00039	1129	1953	GADX	0/0	100.0	97.9	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00004	173073	173486	HNS	0/0	100.0	99.5	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00017	8282	8954	KDPE	0/0	99.3	97.2	MEG_3448	Drugs:Aminoglycosides:Aminoglycoside_efflux_pumps:KDPE	NA
contig00031	22697	23086	MARA	0/0	100.0	99.5	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00031	22249	22683	MARR	0/0	100.0	98.2	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00003	33623	34855	MDFA	0/0	100.0	98.9	MEG_3737	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDFA	NA
contig00007	132092	133339	MDTA	0/0	100.0	98.2	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00007	128970	132092	MDTB	0/0	100.0	99.8	MEG_3747	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTB	NA
contig00007	125892	128969	MDTC	0/0	100.0	98.6	MEG_3749	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTC	NA
contig00039	6550	7707	MDTE	0/0	100.0	99.7	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00039	3412	6525	MDTF	0/0	100.0	98.4	MEG_3752	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTF	NA
contig00015	86688	87914	MDTG	0/0	100.0	99.5	MEG_3753	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig00015	76849	78057	MDTH	0/0	100.0	98.4	MEG_3755	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTH	NA
contig00022	39088	39417	MDTI	0/0	100.0	99.4	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00022	39404	39769	MDTJ	0/0	100.0	99.2	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00011	131056	132429	MDTK	0/0	100.0	99.0	MEG_3759	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:MDTK	NA
contig00005	220370	221602	MDTM	0/0	100.0	96.3	MEG_3761	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTM	NA
contig00036	26171	27202	MDTN	0/0	100.0	98.1	MEG_3763	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN	NA
contig00036	24120	26171	MDTO	0/0	100.0	98.4	MEG_3764	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTO	NA
contig00036	22657	24123	MDTP	0/0	100.0	98.2	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig00092	68	989	MPHA	1/1	100.0	99.7	MEG_4030	Drugs:MLS:Macrolide_phosphotransferases:MPHA	NA
contig00002	243431	243905	MPHB	0/0	99.6	97.5	MEG_4033	Drugs:MLS:Macrolide_phosphotransferases:MPHB	NA
contig00003	133636	135384	MSBA	0/0	100.0	99.4	MEG_4061	Drugs:Multi-drug_resistance:Multi-drug_ABC_efflux_pumps:MSBA	NA
contig00032	2794	3126	MVRC	0/0	100.0	91.9	MEG_4103	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MVRC	NA
contig00017	61082	62983	PBP2	0/0	100.0	99.0	MEG_5400	Drugs:betalactams:Penicillin_binding_protein:PBP2	NA
contig00002	186659	187963	PBP4B	0/0	100.0	98.6	MEG_5409	Drugs:betalactams:Penicillin_binding_protein:PBP4B	NA
contig00002	17662	18630	PMRF	0/0	100.0	99.3	MEG_5801	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF	NA
contig00005	156450	157319	ROBA	0/0	100.0	99.0	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00036	719	1041	SOXS	0/0	99.7	99.7	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00064	3785	4752	SULI	0/0	100.0	100.0	MEG_6615	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULI	NA
contig00077	1684	2958	TETA	0/0	100.0	100.0	MEG_7024	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETA	NA
contig00024	42512	44155	YOGI	0/0	100.0	98.1	MEG_7842	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:YOGI	NA

ID066II

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00898	1945	2805	aac(3)-IIa_1	0/0	100.0	99.8	X51534	aac(3)-IIa	Gentamicin, Tobramycin
contig01356	823	1683	aac(3)-IId_1	0/0	100.0	99.9	EU022314	aac(3)-IId	Gentamicin, Tobramycin
contig01151	1539	2138	aac(6’)-Ib-cr_1	0/0	100.0	100.0	DQ303918	aac(6’)-Ib-cr	Ciprofloxacin
contig00360	1522	2310	aadA5_1	0/0	100.0	100.0	AF137361	aadA5	Streptomycin
contig01094	843	1646	aph(3’’)-Ib_5	0/0	100.0	100.0	AF321551	aph(3’’)-Ib	Streptomycin
contig01094	7	843	aph(6)-Id_1	0/0	100.0	99.9	M28829	aph(6)-Id	Streptomycin
contig01278	416	1291	blaCTX-M-15_1	0/0	100.0	100.0	AY044436	blaCTX-M-15	Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig01151	578	1408	blaOXA-1_1	0/0	100.0	100.0	HQ170510	blaOXA-1	Amoxicillin, Amoxicillin+Clavulanic_acid, Ampicillin, Ampicillin+Clavulanic_acid, Cefepime, Piperacillin, Piperacillin+Tazobactam
contig00470	3103	3963	blaTEM-1B_1	0/0	100.0	100.0	AY458016	blaTEM-1B	Amoxicillin, Ampicillin, Cephalothin, Piperacillin, Ticarcillin
contig00360	918	1391	dfrA17_1	0/0	100.0	100.0	FJ460238	dfrA17	Trimethoprim
contig00659	2526	3758	mdf(A)_1	0/0	100.0	99.9	Y08743	mdf(A)
contig00360	2830	3696	sul1_5	0/0	100.0	99.9	EU780013	sul1	Sulfamethoxazole
contig00820	970	2216	tet(A)_6	0/0	97.8	100.0	AF534183	tet(A)	Doxycycline, Tetracycline
contig00598	750	1955	tet(B)_2	0/0	100.0	100.0	AF326777	tet(B)	Doxycycline, Tetracycline, Minocycline

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig01356	823	1683	AAC(3)-IId	0/0	100.0	99.9	EU022314.1:0-861	AAC(3)-IId is a plasmid-encoded aminoglycoside acetyltransferase in E. coli	aminoglycoside
contig00898	1945	2805	AAC(3)-IIe	0/0	100.0	99.5	EU022315.1:0-861	AAC(3)-IIe is a plasmid-encoded aminoglycoside acetyltransferase in E. coli	aminoglycoside
contig01151	1539	2138	AAC(6’)-Ib-cr	0/0	100.0	100.0	DQ303918:0-600	AAC(6’)-Ib-cr is an aminoglycoside acetyltransferase encoded by plasmids transposons integrons in Enterobacteriaceae. The aac(6’)-Ib-cr variant gene can induce resistance against aminoglycoside and fluoroquinolone simultaneously	aminoglycoside, fluoroquinolone
contig00360	1522	2310	aadA5	0/0	100.0	100.0	AF137361:63-852	aadA5 is an aminoglycoside nucleotidyltransferase gene encoded by plasmids transposons and integrons in E. coli K. pneumoniae Kluyvera georgiana P. aeruginosa and E. cloacae	aminoglycoside
contig00802	167	3206	acrB	0/0	96.5	100.0	U00096.3:484403-481253	Protein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug/proton antiporter.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00295	1934	5047	acrD	0/0	100.0	98.8	AP009048.1:2586250-2589364	AcrD is an aminoglycoside efflux pump expressed in E. coli. Its expression can be induced by indole and is regulated by baeRS and cpxAR.	aminoglycoside
contig00311	1663	4776	acrD	0/0	100.0	98.5	AP009048.1:2586250-2589364	AcrD is an aminoglycoside efflux pump expressed in E. coli. Its expression can be induced by indole and is regulated by baeRS and cpxAR.	aminoglycoside
contig01144	181	1338	acrE	0/0	100.0	98.7	U00096:3413863-3415021	AcrE is a membrane fusion protein similar to AcrA.	cephalosporin, cephamycin, fluoroquinolone, penam
contig01094	843	1646	APH(3’’)-Ib	0/0	100.0	99.8	AF313472:15593-16397	APH(3’’)-Ib is an aminoglycoside phosphotransferase encoded by plasmids transposons integrative conjugative elements and chromosomes in Enterobacteriaceae and Pseudomonas spp.	aminoglycoside
contig01094	7	843	APH(6)-Id	0/0	100.0	99.8	AF024602:3155-3992	APH(6)-Id is an aminoglycoside phosphotransferase encoded by plasmids integrative conjugative elements and chromosomal genomic islands in K. pneumoniae Salmonella spp. E. coli Shigella flexneri Providencia alcalifaciens Pseudomonas spp. V. cholerae Edwardsiella tarda Pasteurella multocida and Aeromonas bestiarum	aminoglycoside
contig01005	280	1099	bacA	0/0	99.8	98.5	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig01534	419	1240	bacA	0/0	100.0	100.0	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00082	11294	12016	baeR	0/0	100.0	100.0	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00732	223	944	baeR	0/0	99.9	96.7	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00082	9894	11297	baeS	0/0	100.0	100.0	AP009048:2165012-2166416	BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.	aminocoumarin, aminoglycoside
contig00732	941	2344	baeS	0/0	100.0	90.6	AP009048:2165012-2166416	BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.	aminocoumarin, aminoglycoside
contig00717	2943	3538	CRP	0/0	94.2	99.8	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig01278	416	1291	CTX-M-15	0/0	100.0	100.0	AY044436:1435-2311	CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family	cephalosporin
contig00360	918	1391	dfrA17	0/0	100.0	100.0	DQ838665:0-474	dfrA17 is an integron-encoded dihydrofolate reductase found in Escherichia coli	diaminopyrimidine
contig00661	1008	2180	emrA	0/0	100.0	98.1	AP009048:2810082-2811255	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	fluoroquinolone
contig00402	999	2537	emrB	0/0	100.0	98.6	U00096:2812615-2814154	emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin.	fluoroquinolone
contig00661	2197	3735	emrB	0/0	100.0	98.1	U00096:2812615-2814154	emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin.	fluoroquinolone
contig00390	3343	4398	emrK	0/0	100.0	98.0	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00456	3330	4385	emrK	0/0	100.0	97.3	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00661	351	881	emrR	0/0	100.0	98.5	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00390	1805	3343	emrY	0/0	100.0	97.7	D78168:1591-3130	emrY is a multidrug transport that moves substrates across the inner membrane of the Gram-negative E. coli. It is a homolog of emrB.	tetracycline
contig00456	1792	3330	emrY	0/0	100.0	97.7	D78168:1591-3130	emrY is a multidrug transport that moves substrates across the inner membrane of the Gram-negative E. coli. It is a homolog of emrB.	tetracycline
contig00644	1515	3158	eptA	0/0	100.0	91.1	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00395	2654	3787	Escherichia_coli_ampC	0/0	100.0	98.0	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00051	11026	12330	Escherichia_coli_ampC1_beta-lactamase	0/0	100.0	95.9	FN649414.1:2765050-2766355	An ampC-like beta-lactamase identified from Escherichia coli.	cephalosporin, penam
contig00416	202	1359	Escherichia_coli_ampH	0/0	100.0	100.0	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig00488	3646	4768	Escherichia_coli_ampH	0/0	97.0	97.2	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig00659	2526	3758	Escherichia_coli_mdfA	0/0	100.0	98.4	JQ394987:0-1233	Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter.	benzalkonium_chloride, rhodamine, tetracycline
contig00390	4922	5536	evgA	0/0	100.0	99.2	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00013	1613	2341	gadW	0/0	100.0	94.7	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig00688	178	906	gadW	0/0	100.0	99.7	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig00013	421	1245	gadX	0/0	100.0	100.0	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig01848	363	1143	gadX	0/0	94.7	93.6	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00074	5134	5811	kdpE	0/0	100.0	100.0	U00096.3:721733-721055	kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding.	aminoglycoside
contig00175	5134	5806	kdpE	0/0	99.3	95.8	U00096.3:721733-721055	kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding.	aminoglycoside
contig00472	953	1336	marA	0/0	100.0	100.0	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig01750	701	1084	marA	0/0	100.0	98.4	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00082	1034	2281	mdtA	0/0	100.0	98.0	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00710	793	2040	mdtA	0/0	100.0	95.7	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00082	2281	5403	mdtB	0/0	100.0	99.7	U00096:2155262-2158385	MdtB is a transporter that forms a heteromultimer complex with MdtC to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex.	aminocoumarin
contig00082	5404	8481	mdtC	0/0	100.0	99.8	U00096:2158385-2161463	MdtC is a transporter that forms a heteromultimer complex with MdtB to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex. In the absence of MdtB MdtC can form a homomultimer complex that results in a functioning efflux complex with a narrower drug specificity. mdtC corresponds to 3 loci in Pseudomonas aeruginosa PAO1 (gene name: muxC/muxB) and 3 loci in Pseudomonas aeruginosa LESB58.	aminocoumarin
contig00513	17	3094	mdtC	0/0	100.0	93.9	U00096:2158385-2161463	MdtC is a transporter that forms a heteromultimer complex with MdtB to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex. In the absence of MdtB MdtC can form a homomultimer complex that results in a functioning efflux complex with a narrower drug specificity. mdtC corresponds to 3 loci in Pseudomonas aeruginosa PAO1 (gene name: muxC/muxB) and 3 loci in Pseudomonas aeruginosa LESB58.	aminocoumarin
contig00013	5842	6999	mdtE	0/0	100.0	100.0	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00815	726	1883	mdtE	0/0	100.0	98.5	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00013	2704	5817	mdtF	0/0	100.0	100.0	U00096:3660413-3663527	MdtF is the multidrug inner membrane transporter for the MdtEF-TolC efflux complex.	fluoroquinolone, macrolide, penam
contig00481	340	1566	mdtG	0/0	100.0	99.4	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig01373	522	1730	mdtH	0/0	100.0	99.9	U00096:1125326-1124117	Multidrug resistance protein MdtH	fluoroquinolone
contig00703	1575	2807	mdtM	0/0	100.0	96.3	U00096.3:4568519-4567286	Multidrug resistance protein MdtM	acridine_dye, fluoroquinolone, lincosamide, nucleoside, phenicol
contig00296	3571	4602	mdtN	0/0	100.0	100.0	AP009048.1:4307588-4306556	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	acridine_dye, nucleoside
contig00296	4602	6653	mdtO	0/0	100.0	100.0	AP009048.1:4306557-4304505	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00540	876	2927	mdtO	0/0	100.0	97.1	AP009048.1:4306557-4304505	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00540	2924	4387	mdtP	0/0	99.8	97.7	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00039	10459	10933	mphB	0/0	99.6	96.2	AE005174.2:3397370-3397847	The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides.	macrolide
contig00178	3202	4950	msbA	0/0	100.0	100.0	U00096.3:966620-968369	MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability.	nitroimidazole
contig01151	578	1408	OXA-1	0/0	100.0	100.0	JN420336.1:2230-1399	OXA-1 is a beta-lactamase found in E. coli	cephalosporin, penam
contig00398	2192	3160	pmrF	0/0	100.0	98.0	U00096:2367070-2368039	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide
contig00881	1937	2905	pmrF	0/0	100.0	97.7	U00096:2367070-2368039	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide
contig00360	2857	3696	sul1	0/0	100.0	100.0	JF969163:1053-1893	Sul1 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria. It is linked to other resistance genes of class 1 integrons.	sulfonamide
contig00470	3103	3963	TEM-1	0/0	100.0	99.9	AL513383:161910-162771	TEM-1 is a broad-spectrum beta-lactamase found in many Gram-negative bacteria. Confers resistance to penicillins and first generation cephalosphorins.	cephalosporin, monobactam, penam, penem
contig00820	970	2216	tet(A)	0/0	97.8	100.0	AF534183.1:2970-4245	TetA is a tetracycline efflux pump found in many species of Gram-negative bacteria.	tetracycline
contig00598	750	1955	tet(B)	0/0	100.0	99.8	AB089595:0-1206	Tet(B) is a tetracycline efflux protein expressed in many Gram-negative bacteria. It confers resistance to tetracycline doxycycline and minocycline but not tigecycline.	tetracycline
contig00226	4598	5764	ugd	0/0	100.0	97.0	U00096:2099613-2098446	PmrE is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00898	1945	2805	(AGly)aac3-IIa	0/0	100.0	99.8	X51534:91-951	(AGly)aac3-IIa	NA
contig01356	823	1683	(AGly)aac3-IId	0/0	100.0	99.9	EU022314:1-861	(AGly)aac3-IId	NA
contig00360	1522	2310	(AGly)aadA5	0/0	100.0	100.0	AF137361:64-852	(AGly)aadA5	NA
contig01094	843	1646	(AGly)strA	0/0	100.0	99.9	AB366441:22458-23261	(AGly)strA	NA
contig01094	7	843	(AGly)strB	0/0	100.0	99.9	FJ474091:264-1100	(AGly)strB	NA
contig00051	11026	12330	(Bla)AmpC1_Ecoli	0/0	100.0	95.9	FN649414:2765051-2766355	(Bla)AmpC1_Ecoli	NA
contig00395	2654	3787	(Bla)AmpC2_Ecoli	0/0	100.0	98.0	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00416	202	1359	(Bla)ampH_Ecoli	0/0	100.0	100.0	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00488	3646	4768	(Bla)ampH_Ecoli	0/0	97.0	97.2	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig01278	416	1291	(Bla)blaCTX-M-15	0/0	100.0	100.0	JQ686199:261-1136	(Bla)blaCTX-M-15	NA
contig01151	578	1408	(Bla)blaOXA-1	0/0	100.0	100.0	JQ682867:1-831	(Bla)blaOXA-1	NA
contig00470	3103	3963	(Bla)blaTEM-105	0/0	100.0	99.9	AF516720:215-1075	(Bla)blaTEM-105	NA
contig00884	141	2042	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100.0	100.0	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA
contig00360	2857	3696	(Sul)sul1	0/0	100.0	100.0	AF071413:6700-7539	(Sul)sul1	NA
contig00820	970	2244	(Tet)tetA	0/0	100.0	100.0	JX424423:94438-95712	(Tet)tetA	NA
contig00598	750	1955	(Tet)tetB	0/0	100.0	99.7	AB089594:1-1206	(Tet)tetB	NA
contig00820	313	939	(Tet)tetR	1/24	96.3	96.3	HF545434:53576-54226	(Tet)tetR	NA
contig00360	918	1391	(Tmt)dfrA17	0/0	100.0	100.0	AB126604:98-571	(Tmt)dfrA17	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig01356	823	1683	aac(3)-IId	0/0	100	100.0	NG_047251.1	aminoglycoside N-acetyltransferase AAC(3)-IId	GENTAMICIN
contig00898	1945	2805	aac(3)-IIe	0/0	100	99.8	NG_047244.1	aminoglycoside N-acetyltransferase AAC(3)-IIe	GENTAMICIN
contig01151	1539	2093	aac(6’)-Ib-D181Y	0/0	100	99.8	NG_067946.1	AAC(6’)-Ib family aminoglycoside 6’-N-acetyltransferase	AMIKACIN, KANAMYCIN, TOBRAMYCIN
contig00360	1522	2310	aadA5	0/0	100	100.0	NG_047357.1	ANT(3’’)-Ia family aminoglycoside nucleotidyltransferase AadA5	STREPTOMYCIN
contig01094	843	1670	aph(3’’)-Ib	0/0	100	100.0	NG_056002.2	aminoglycoside O-phosphotransferase APH(3’’)-Ib	STREPTOMYCIN
contig01094	7	843	aph(6)-Id	0/0	100	100.0	NG_047466.1	aminoglycoside O-phosphotransferase APH(6)-Id	STREPTOMYCIN
contig01278	416	1291	blaCTX-M-15	0/0	100	100.0	NG_048935.1	class A extended-spectrum beta-lactamase CTX-M-15	CEPHALOSPORIN
contig00395	2654	3787	blaEC-5	0/0	100	99.8	NG_049085.1	cephalosporin-hydrolyzing class C beta-lactamase EC-5	CEPHALOSPORIN
contig01151	578	1408	blaOXA-1	0/0	100	100.0	NG_049392.1	oxacillin-hydrolyzing class D beta-lactamase OXA-1	CEPHALOSPORIN
contig00470	3103	3963	blaTEM-1	0/0	100	100.0	NG_050145.1	class A broad-spectrum beta-lactamase TEM-1	BETA-LACTAM
contig00360	918	1391	dfrA17	0/0	100	99.8	NG_047710.1	trimethoprim-resistant dihydrofolate reductase DfrA17	TRIMETHOPRIM
contig00360	2857	3696	sul1	0/0	100	100.0	NG_048082.1	sulfonamide-resistant dihydropteroate synthase Sul1	SULFONAMIDE
contig00820	1045	2244	tet(A)	0/0	100	100.0	NG_048154.1	tetracycline efflux MFS transporter Tet(A)	TETRACYCLINE
contig00598	750	1955	tet(B)	0/0	100	100.0	NG_048163.1	tetracycline efflux MFS transporter Tet(B)	TETRACYCLINE

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00898	1945	2805	AAC3	0/0	100.0	99.8	MEG_44	Drugs:Aminoglycosides:Aminoglycoside_N-acetyltransferases:AAC3	NA
contig01356	823	1683	AAC3	0/0	100.0	100.0	MEG_64	Drugs:Aminoglycosides:Aminoglycoside_N-acetyltransferases:AAC3	NA
contig00802	167	3206	ACRB	0/0	96.5	100.0	MEG_401	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRB	NA
contig00295	1934	5047	ACRD	0/0	100.0	98.8	MEG_407	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ACRD	NA
contig00311	1663	4776	ACRD	0/0	100.0	98.5	MEG_407	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ACRD	NA
contig01144	181	1338	ACRE	0/0	100.0	98.7	MEG_408	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRE	NA
contig00416	202	1359	AMPH	0/0	100.0	100.0	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00488	3646	4768	AMPH	0/0	97.0	97.2	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00360	1522	2310	ANT3-DPRIME	0/0	100.0	100.0	MEG_928	Drugs:Aminoglycosides:Aminoglycoside_O-nucleotidyltransferases:ANT3-DPRIME	NA
contig01094	843	1670	APH3-DPRIME	0/0	100.0	100.0	MEG_1019	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH3-DPRIME	NA
contig01094	7	843	APH6	0/0	100.0	100.0	MEG_1084	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH6	NA
contig01005	280	1099	BACA	0/0	99.8	98.8	MEG_1189	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig01534	419	1240	BACA	0/0	100.0	100.0	MEG_1190	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00082	11294	12016	BAER	0/0	100.0	100.0	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00732	223	944	BAER	0/0	99.9	96.7	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00082	9894	11297	BAES	0/0	100.0	100.0	MEG_1193	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES	NA
contig00732	941	2344	BAES	0/0	100.0	90.6	MEG_1193	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES	NA
contig00198	4773	5963	BCR	0/0	100.0	100.0	MEG_1210	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR	NA
contig00395	2654	3787	BLAEC	0/0	100.0	99.8	MEG_1275	Drugs:betalactams:Class_C_betalactamases:BLAEC	NA
contig00704	2406	3104	CPXAR	0/0	100.0	100.0	MEG_2122	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00717	2943	3538	CRP	0/0	94.2	99.8	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig01989	62	1004	CTX	0/0	100.0	98.2	MEG_2435	Drugs:betalactams:Class_A_betalactamases:CTX	NA
contig00360	918	1391	DFRA	0/0	100.0	100.0	MEG_2547	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00661	1008	2180	EMRA	0/0	100.0	98.1	MEG_2722	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA	NA
contig00402	999	2537	EMRB	0/0	100.0	98.6	MEG_2725	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRB	NA
contig00661	2197	3735	EMRB	0/0	100.0	98.1	MEG_2725	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRB	NA
contig01139	401	1591	EMRD	0/0	100.0	100.0	MEG_2729	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD	NA
contig00390	3343	4506	EMRK	0/0	100.0	98.2	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig00456	3330	4493	EMRK	0/0	100.0	97.2	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig00661	351	881	EMRR	0/0	100.0	98.5	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00390	1805	3343	EMRY	0/0	100.0	97.7	MEG_2736	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRY	NA
contig00456	1792	3330	EMRY	0/0	100.0	97.8	MEG_2736	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRY	NA
contig00644	1515	3158	EPTA	0/0	100.0	91.1	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig00013	1613	2341	GADW	0/0	100.0	100.0	MEG_3081	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig00688	178	906	GADW	0/0	100.0	99.7	MEG_3082	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig00013	421	1245	GADX	0/0	100.0	100.0	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig01848	363	1143	GADX	0/0	94.7	93.6	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00074	5134	5811	KDPE	0/0	100.0	100.0	MEG_3448	Drugs:Aminoglycosides:Aminoglycoside_efflux_pumps:KDPE	NA
contig00175	5134	5806	KDPE	0/0	99.3	95.8	MEG_3448	Drugs:Aminoglycosides:Aminoglycoside_efflux_pumps:KDPE	NA
contig00472	947	1336	MARA	0/0	100.0	100.0	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig01750	695	1084	MARA	0/0	100.0	98.5	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00472	499	933	MARR	0/0	100.0	100.0	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig01750	246	680	MARR	0/0	100.0	98.2	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00659	2526	3758	MDFA	0/0	100.0	100.0	MEG_3737	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDFA	NA
contig00082	1034	2281	MDTA	0/0	100.0	98.0	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00710	793	2040	MDTA	0/0	100.0	95.7	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00082	2281	5403	MDTB	0/0	100.0	99.7	MEG_3747	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTB	NA
contig00082	5404	8481	MDTC	0/0	100.0	99.8	MEG_3749	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTC	NA
contig00513	17	3094	MDTC	0/0	100.0	93.9	MEG_3749	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTC	NA
contig00013	5842	6999	MDTE	0/0	100.0	100.0	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00815	726	1883	MDTE	0/0	100.0	98.5	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00013	2704	5817	MDTF	0/0	100.0	100.0	MEG_3752	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTF	NA
contig00481	340	1566	MDTG	0/0	100.0	100.0	MEG_3753	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig01373	522	1730	MDTH	0/0	100.0	99.9	MEG_3755	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTH	NA
contig00909	595	924	MDTI	0/0	100.0	100.0	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig01093	595	924	MDTI	0/0	100.0	98.8	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00909	243	608	MDTJ	0/0	100.0	99.5	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig01093	243	608	MDTJ	0/0	100.0	97.5	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00703	1575	2807	MDTM	0/0	100.0	96.3	MEG_3761	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTM	NA
contig00296	3571	4602	MDTN	0/0	100.0	100.0	MEG_3763	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN	NA
contig00296	4602	6653	MDTO	0/0	100.0	100.0	MEG_3764	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTO	NA
contig00540	876	2927	MDTO	0/0	100.0	97.1	MEG_3764	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTO	NA
contig00540	2924	4387	MDTP	0/0	99.8	97.7	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig00039	10459	10933	MPHB	0/0	99.6	96.2	MEG_4033	Drugs:MLS:Macrolide_phosphotransferases:MPHB	NA
contig00178	3202	4950	MSBA	0/0	100.0	100.0	MEG_4061	Drugs:Multi-drug_resistance:Multi-drug_ABC_efflux_pumps:MSBA	NA
contig01151	578	1408	OXA	0/0	100.0	100.0	MEG_4980	Drugs:betalactams:Class_D_betalactamases:OXA	NA
contig00884	141	2042	PBP2	0/0	100.0	100.0	MEG_5400	Drugs:betalactams:Penicillin_binding_protein:PBP2	NA
contig00051	11026	12330	PBP4B	0/0	100.0	95.9	MEG_5409	Drugs:betalactams:Penicillin_binding_protein:PBP4B	NA
contig00398	2192	3160	PMRF	0/0	100.0	98.0	MEG_5801	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF	NA
contig00881	1937	2905	PMRF	0/0	100.0	97.7	MEG_5801	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF	NA
contig00329	4795	5664	ROBA	0/0	100.0	99.0	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00412	3998	4867	ROBA	0/0	100.0	97.2	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00360	2856	3823	SULI	0/0	100.0	100.0	MEG_6615	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULI	NA
contig00470	3085	4330	TEM	0/0	98.3	99.4	MEG_6875	Drugs:betalactams:Class_A_betalactamases:TEM	NA
contig00820	970	2244	TETA	0/0	100.0	100.0	MEG_7024	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETA	NA
contig00598	750	1955	TETB	0/0	100.0	100.0	MEG_7052	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETB	NA
contig00598	2749	3165	TETD	0/0	100.0	100.0	MEG_7070	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETD	NA
contig00226	4598	5764	UGD	0/0	100.0	97.0	MEG_7328	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:UGD	NA

ID067

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00049	23105	23908	aph(3’’)-Ib_5	0/0	100.0	100.0	AF321551	aph(3’’)-Ib	Streptomycin
contig00049	22269	23105	aph(6)-Id_1	0/0	100.0	100.0	M28829	aph(6)-Id	Streptomycin
contig00049	16991	17866	blaCTX-M-15_1	0/0	100.0	100.0	AY044436	blaCTX-M-15	Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig00049	20688	21548	blaTEM-1B_1	0/0	100.0	100.0	AY458016	blaTEM-1B	Amoxicillin, Ampicillin, Cephalothin, Piperacillin, Ticarcillin
contig00092	181	663	dfrA14_5	0/0	100.0	99.4	DQ388123	dfrA14	Trimethoprim
contig00010	2389	3621	mdf(A)_1	0/0	100.0	99.3	Y08743	mdf(A)
contig00049	11694	12350	qnrS1_1	0/0	100.0	100.0	AB187515	qnrS1	Ciprofloxacin
contig00049	23969	24784	sul2_2	0/0	100.0	100.0	AY034138	sul2	Sulfamethoxazole
contig00083	3242	4488	tet(A)_6	0/0	97.8	100.0	AF534183	tet(A)	Doxycycline, Tetracycline

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00005	88485	91634	acrB	0/0	100.0	99.4	U00096.3:484403-481253	Protein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug/proton antiporter.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00001	183201	186314	acrD	0/0	100.0	99.3	AP009048.1:2586250-2589364	AcrD is an aminoglycoside efflux pump expressed in E. coli. Its expression can be induced by indole and is regulated by baeRS and cpxAR.	aminoglycoside
contig00003	140117	141274	acrE	0/0	100.0	99.0	U00096:3413863-3415021	AcrE is a membrane fusion protein similar to AcrA.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00003	141286	144390	acrF	0/0	100.0	99.0	U00096:3415032-3418137	AcrF is a inner membrane transporter similar to AcrB.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00003	139056	139718	acrS	0/0	100.0	99.1	U00096:3413465-3412802	AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.	cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00049	23105	23908	APH(3’’)-Ib	0/0	100.0	99.8	AF313472:15593-16397	APH(3’’)-Ib is an aminoglycoside phosphotransferase encoded by plasmids transposons integrative conjugative elements and chromosomes in Enterobacteriaceae and Pseudomonas spp.	aminoglycoside
contig00049	22269	23105	APH(6)-Id	0/0	100.0	99.9	AF024602:3155-3992	APH(6)-Id is an aminoglycoside phosphotransferase encoded by plasmids integrative conjugative elements and chromosomal genomic islands in K. pneumoniae Salmonella spp. E. coli Shigella flexneri Providencia alcalifaciens Pseudomonas spp. V. cholerae Edwardsiella tarda Pasteurella multocida and Aeromonas bestiarum	aminoglycoside
contig00064	11886	12707	bacA	0/0	100.0	100.0	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00026	38666	39388	baeR	0/0	100.0	100.0	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00026	37266	38669	baeS	0/0	100.0	100.0	AP009048:2165012-2166416	BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.	aminocoumarin, aminoglycoside
contig00022	61701	63074	cpxA	0/0	100.0	98.7	BA000007.3:4905062-4903688	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	aminocoumarin, aminoglycoside
contig00015	15012	15644	CRP	0/0	100.0	99.4	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00049	16991	17866	CTX-M-15	0/0	100.0	100.0	AY044436:1435-2311	CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family	cephalosporin
contig00092	181	663	dfrA14	0/0	100.0	99.6	EU780012:2162-2645	dfrA14 is an integron-encoded dihydrofolate reductase found in Escherichia coli	diaminopyrimidine
contig00012	37589	38761	emrA	0/0	100.0	100.0	AP009048:2810082-2811255	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	fluoroquinolone
contig00012	38778	40316	emrB	0/0	100.0	100.0	U00096:2812615-2814154	emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin.	fluoroquinolone
contig00001	84977	86032	emrK	0/0	100.0	99.9	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00012	36932	37462	emrR	0/0	100.0	100.0	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00001	83439	84977	emrY	0/0	100.0	99.0	D78168:1591-3130	emrY is a multidrug transport that moves substrates across the inner membrane of the Gram-negative E. coli. It is a homolog of emrB.	tetracycline
contig00025	24538	26181	eptA	0/0	100.0	99.8	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00005	91657	92850	Escherichia_coli_acrA	0/0	100.0	100.0	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00008	129825	130958	Escherichia_coli_ampC	0/0	100.0	97.3	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00001	145408	146712	Escherichia_coli_ampC1_beta-lactamase	0/0	100.0	99.1	FN649414.1:2765050-2766355	An ampC-like beta-lactamase identified from Escherichia coli.	cephalosporin, penam
contig00005	2471	3628	Escherichia_coli_ampH	0/0	100.0	98.9	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig00040	32107	32439	Escherichia_coli_emrE	0/0	100.0	91.9	Z11877.1:485-818	Member of the small MDR (multidrug resistance) family of transporters, in Escherichia coli this protein provides resistance against a number of positively charged compounds including ethidium bromide and erythromycin, proton-dependent secondary transporter which exchanges protons for compound translocation	macrolide
contig00010	2389	3621	Escherichia_coli_mdfA	0/0	100.0	97.8	JQ394987:0-1233	Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter.	benzalkonium_chloride, rhodamine, tetracycline
contig00001	86556	87170	evgA	0/0	100.0	100.0	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00001	87175	90768	evgS	0/0	100.0	99.9	U00096:2484373-2487967	EvgS is a sensor protein that phosphorylates the regulatory protein EvgA. evgS corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	fluoroquinolone, macrolide, penam, tetracycline
contig00020	31791	32519	gadW	0/0	100.0	94.7	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig00020	30599	31423	gadX	0/0	100.0	100.0	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00034	5364	5777	H-NS	0/0	100.0	99.0	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00060	9569	10246	kdpE	0/0	100.0	99.1	U00096.3:721733-721055	kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding.	aminoglycoside
contig00068	3021	3404	marA	0/0	100.0	100.0	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00026	28406	29653	mdtA	0/0	100.0	99.8	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00026	29653	32775	mdtB	0/0	100.0	99.8	U00096:2155262-2158385	MdtB is a transporter that forms a heteromultimer complex with MdtC to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex.	aminocoumarin
contig00026	32776	35853	mdtC	0/0	100.0	99.8	U00096:2158385-2161463	MdtC is a transporter that forms a heteromultimer complex with MdtB to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex. In the absence of MdtB MdtC can form a homomultimer complex that results in a functioning efflux complex with a narrower drug specificity. mdtC corresponds to 3 loci in Pseudomonas aeruginosa PAO1 (gene name: muxC/muxB) and 3 loci in Pseudomonas aeruginosa LESB58.	aminocoumarin
contig00020	36020	37177	mdtE	0/0	100.0	99.9	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00020	32882	35995	mdtF	0/0	100.0	100.0	U00096:3660413-3663527	MdtF is the multidrug inner membrane transporter for the MdtEF-TolC efflux complex.	fluoroquinolone, macrolide, penam
contig00073	2961	4187	mdtG	0/0	100.0	99.7	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00007	127619	128827	mdtH	0/0	100.0	98.3	U00096:1125326-1124117	Multidrug resistance protein MdtH	fluoroquinolone
contig00017	71160	72391	mdtM	1/1	99.9	96.2	U00096.3:4568519-4567286	Multidrug resistance protein MdtM	acridine_dye, fluoroquinolone, lincosamide, nucleoside, phenicol
contig00014	5198	6229	mdtN	0/0	100.0	100.0	AP009048.1:4307588-4306556	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	acridine_dye, nucleoside
contig00014	6229	8280	mdtO	0/0	100.0	99.1	AP009048.1:4306557-4304505	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00014	8277	9743	mdtP	0/0	100.0	100.0	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00001	206992	207468	mphB	0/0	100.0	98.3	AE005174.2:3397370-3397847	The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides.	macrolide
contig00009	50809	52557	msbA	0/0	100.0	100.0	U00096.3:966620-968369	MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability.	nitroimidazole
contig00019	15348	16316	pmrF	0/0	100.0	99.6	U00096:2367070-2368039	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide
contig00049	11694	12350	QnrS1	0/0	100.0	100.0	DQ485529.1:0-657	QnrS1 is a plasmid-mediated quinolone resistance protein found in Shigella flexneri	fluoroquinolone
contig00049	23969	24784	sul2	0/0	100.0	100.0	AY055428.1:21084-20268	Sul2 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria usually found on small plasmids.	sulfonamide
contig00049	20688	21548	TEM-1	0/0	100.0	99.9	AL513383:161910-162771	TEM-1 is a broad-spectrum beta-lactamase found in many Gram-negative bacteria. Confers resistance to penicillins and first generation cephalosphorins.	cephalosporin, monobactam, penam, penem
contig00083	3242	4488	tet(A)	0/0	97.8	100.0	AF534183.1:2970-4245	TetA is a tetracycline efflux pump found in many species of Gram-negative bacteria.	tetracycline
contig00006	126983	128470	tolC	0/0	100.0	99.7	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan
contig00019	74578	76221	yojI	0/0	100.0	99.7	U00096.3:2308615-2306971	YojI mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. YojI is capable of pumping out microcin molecules. The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI.	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00049	23105	23908	(AGly)strA	0/0	100	99.9	AB366441:22458-23261	(AGly)strA	NA
contig00049	22269	23105	(AGly)strB	0/0	100	100.0	FJ474091:264-1100	(AGly)strB	NA
contig00001	145408	146712	(Bla)AmpC1_Ecoli	0/0	100	99.1	FN649414:2765051-2766355	(Bla)AmpC1_Ecoli	NA
contig00008	129825	130958	(Bla)AmpC2_Ecoli	0/0	100	97.3	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00005	2471	3628	(Bla)ampH_Ecoli	0/0	100	98.9	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00049	16991	17866	(Bla)blaCTX-M-15	0/0	100	100.0	JQ686199:261-1136	(Bla)blaCTX-M-15	NA
contig00049	20688	21548	(Bla)blaTEM-105	0/0	100	99.9	AF516720:215-1075	(Bla)blaTEM-105	NA
contig00016	34560	36461	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100	99.4	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA
contig00049	11694	12350	(Flq)qnr-S1	0/0	100	100.0	AB187515:9737-10393	(Flq)qnr-S1	NA
contig00049	23969	24784	(Sul)sul2	0/0	100	100.0	EU360945:1617-2432	(Sul)sul2	NA
contig00083	3214	4488	(Tet)tetA	0/0	100	100.0	JX424423:94438-95712	(Tet)tetA	NA
contig00083	4519	5169	(Tet)tetR	0/0	100	100.0	HF545434:53576-54226	(Tet)tetR	NA
contig00092	181	654	(Tmt)dfrA14	0/0	100	99.8	GU726917:72-545	(Tmt)dfrA14	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00049	23105	23932	aph(3’’)-Ib	0/0	100	100.0	NG_056002.2	aminoglycoside O-phosphotransferase APH(3’’)-Ib	STREPTOMYCIN
contig00049	22269	23105	aph(6)-Id	0/0	100	100.0	NG_047464.1	aminoglycoside O-phosphotransferase APH(6)-Id	STREPTOMYCIN
contig00049	16991	17866	blaCTX-M-15	0/0	100	100.0	NG_048935.1	class A extended-spectrum beta-lactamase CTX-M-15	CEPHALOSPORIN
contig00008	129825	130958	blaEC-15	0/0	100	98.6	NG_049081.1	class C extended-spectrum beta-lactamase EC-15	CEPHALOSPORIN
contig00049	20688	21548	blaTEM-1	0/0	100	100.0	NG_050145.1	class A broad-spectrum beta-lactamase TEM-1	BETA-LACTAM
contig00092	181	654	dfrA14	0/0	100	99.8	NG_056035.1	trimethoprim-resistant dihydrofolate reductase DfrA14	TRIMETHOPRIM
contig00049	11694	12350	qnrS1	0/0	100	100.0	NG_050543.1	quinolone resistance pentapeptide repeat protein QnrS1	QUINOLONE
contig00049	23969	24784	sul2	0/0	100	100.0	NG_051852.1	sulfonamide-resistant dihydropteroate synthase Sul2	SULFONAMIDE
contig00083	3214	4413	tet(A)	0/0	100	100.0	NG_048154.1	tetracycline efflux MFS transporter Tet(A)	TETRACYCLINE

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00005	91657	92850	ACRA	0/0	100.0	100.0	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00005	88485	91634	ACRB	0/0	100.0	99.4	MEG_401	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRB	NA
contig00001	183201	186314	ACRD	0/0	100.0	99.3	MEG_407	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ACRD	NA
contig00003	140117	141274	ACRE	0/0	100.0	99.0	MEG_408	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRE	NA
contig00003	141286	144390	ACRF	0/0	100.0	99.0	MEG_409	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRF	NA
contig00003	139056	139718	ACRS	0/0	100.0	99.1	MEG_415	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS	NA
contig00005	2471	3628	AMPH	0/0	100.0	98.9	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00049	23105	23932	APH3-DPRIME	0/0	100.0	100.0	MEG_1019	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH3-DPRIME	NA
contig00049	22269	23105	APH6	0/0	100.0	100.0	MEG_1086	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH6	NA
contig00026	14151	16003	ASMA	0/0	100.0	97.2	MEG_1180	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:ASMA	NA
contig00064	11886	12707	BACA	0/0	100.0	100.0	MEG_1190	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00026	38666	39388	BAER	0/0	100.0	100.0	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00026	37266	38669	BAES	0/0	100.0	100.0	MEG_1193	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES	NA
contig00011	80954	82144	BCR	0/0	100.0	100.0	MEG_1210	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR	NA
contig00008	129825	130958	BLAEC	0/0	100.0	98.6	MEG_1282	Drugs:betalactams:Class_C_betalactamases:BLAEC	NA
contig00022	61006	61704	CPXAR	0/0	100.0	99.9	MEG_2118	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00022	61701	63074	CPXAR	0/0	100.0	99.4	MEG_2121	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00015	15012	15644	CRP	0/0	100.0	99.4	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00001	154530	155470	CTX	0/0	99.8	91.8	MEG_2435	Drugs:betalactams:Class_A_betalactamases:CTX	NA
contig00072	1653	2595	CTX	0/0	100.0	95.3	MEG_2435	Drugs:betalactams:Class_A_betalactamases:CTX	NA
contig00092	181	654	DFRA	0/0	100.0	99.6	MEG_2517	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00012	37589	38761	EMRA	0/0	100.0	100.0	MEG_2722	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA	NA
contig00012	38778	40316	EMRB	0/0	100.0	100.0	MEG_2725	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRB	NA
contig00063	14218	15408	EMRD	0/0	100.0	99.7	MEG_2729	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD	NA
contig00001	84977	86140	EMRK	0/0	100.0	99.9	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig00012	36932	37462	EMRR	0/0	100.0	100.0	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00001	83439	84977	EMRY	0/0	100.0	99.1	MEG_2736	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRY	NA
contig00025	24538	26181	EPTA	0/0	100.0	99.8	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig00001	87175	90768	EVGS	0/0	100.0	99.9	MEG_2870	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EVGS	NA
contig00020	31791	32519	GADW	0/0	100.0	100.0	MEG_3081	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig00020	30599	31423	GADX	0/0	100.0	100.0	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00034	5364	5777	HNS	0/0	100.0	99.0	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00060	9569	10246	KDPE	0/0	100.0	99.1	MEG_3448	Drugs:Aminoglycosides:Aminoglycoside_efflux_pumps:KDPE	NA
contig00068	3015	3404	MARA	0/0	100.0	100.0	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00068	2567	3001	MARR	0/0	100.0	97.5	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00010	2389	3621	MDFA	0/0	100.0	99.4	MEG_3737	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDFA	NA
contig00026	28406	29653	MDTA	0/0	100.0	99.8	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00026	29653	32775	MDTB	0/0	100.0	99.8	MEG_3747	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTB	NA
contig00026	32776	35853	MDTC	0/0	100.0	99.8	MEG_3749	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTC	NA
contig00020	36020	37177	MDTE	0/0	100.0	99.9	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00020	32882	35995	MDTF	0/0	100.0	100.0	MEG_3752	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTF	NA
contig00073	2961	4187	MDTG	0/0	100.0	99.7	MEG_3754	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig00007	127619	128827	MDTH	0/0	100.0	98.3	MEG_3755	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTH	NA
contig00031	19376	19705	MDTI	0/0	100.0	100.0	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00031	19692	20057	MDTJ	0/0	100.0	99.2	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00023	34638	36011	MDTK	0/0	100.0	98.9	MEG_3759	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:MDTK	NA
contig00017	71160	72391	MDTM	1/1	99.9	96.2	MEG_3761	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTM	NA
contig00014	5198	6229	MDTN	0/0	100.0	100.0	MEG_3763	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN	NA
contig00014	6229	8280	MDTO	0/0	100.0	99.1	MEG_3764	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTO	NA
contig00014	8277	9743	MDTP	0/0	100.0	100.0	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig00001	206992	207468	MPHB	0/0	100.0	98.3	MEG_4033	Drugs:MLS:Macrolide_phosphotransferases:MPHB	NA
contig00009	50809	52557	MSBA	0/0	100.0	100.0	MEG_4061	Drugs:Multi-drug_resistance:Multi-drug_ABC_efflux_pumps:MSBA	NA
contig00040	32107	32439	MVRC	0/0	100.0	91.9	MEG_4103	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MVRC	NA
contig00016	34560	36461	PBP2	0/0	100.0	99.4	MEG_5400	Drugs:betalactams:Penicillin_binding_protein:PBP2	NA
contig00001	145408	146712	PBP4B	0/0	100.0	99.1	MEG_5409	Drugs:betalactams:Penicillin_binding_protein:PBP4B	NA
contig00019	15348	16316	PMRF	0/0	100.0	99.6	MEG_5801	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF	NA
contig00049	11694	12350	QNRS	0/0	100.0	100.0	MEG_6020	Drugs:Fluoroquinolones:Quinolone_resistance_protein_Qnr:QNRS	NA
contig00017	23036	23905	ROBA	0/0	100.0	99.0	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00014	31811	32133	SOXS	0/0	99.7	99.7	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00049	23969	24784	SULII	0/0	100.0	100.0	MEG_6617	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULII	NA
contig00049	20321	21566	TEM	0/0	98.3	99.4	MEG_6875	Drugs:betalactams:Class_A_betalactamases:TEM	NA
contig00083	3214	4488	TETA	0/0	100.0	100.0	MEG_7024	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETA	NA
contig00019	74578	76221	YOGI	0/0	100.0	99.7	MEG_7842	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:YOGI	NA

ID068

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00047	8359	9234	blaCTX-M-15_1	0/0	100.0	100.0	AY044436	blaCTX-M-15	Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig00047	3417	4277	blaTEM-1B_1	0/0	100.0	100.0	AY458016	blaTEM-1B	Amoxicillin, Ampicillin, Cephalothin, Piperacillin, Ticarcillin
contig00078	183	665	dfrA14_5	0/0	100.0	99.6	DQ388123	dfrA14	Trimethoprim
contig00029	30138	31370	mdf(A)_1	0/0	100.0	99.8	Y08743	mdf(A)
contig00047	13875	14531	qnrS1_1	0/0	100.0	100.0	AB187515	qnrS1	Ciprofloxacin
contig00005	109476	110291	sul2_2	0/0	100.0	100.0	AY034138	sul2	Sulfamethoxazole
contig00047	835	2081	tet(A)_6	0/0	97.8	100.0	AF534183	tet(A)	Doxycycline, Tetracycline

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00002	74183	77332	acrB	0/0	100.0	100.0	U00096.3:484403-481253	Protein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug/proton antiporter.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00005	150847	153960	acrD	0/0	100.0	100.0	AP009048.1:2586250-2589364	AcrD is an aminoglycoside efflux pump expressed in E. coli. Its expression can be induced by indole and is regulated by baeRS and cpxAR.	aminoglycoside
contig00023	65865	66686	bacA	0/0	100.0	100.0	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00025	40179	40901	baeR	0/0	100.0	100.0	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00025	38779	40182	baeS	0/0	100.0	100.0	AP009048:2165012-2166416	BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.	aminocoumarin, aminoglycoside
contig00022	61323	62696	cpxA	0/0	100.0	99.0	BA000007.3:4905062-4903688	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	aminocoumarin, aminoglycoside
contig00009	15261	15893	CRP	0/0	100.0	99.7	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00047	8359	9234	CTX-M-15	0/0	100.0	100.0	AY044436:1435-2311	CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family	cephalosporin
contig00078	183	665	dfrA14	0/0	100.0	99.8	EU780012:2162-2645	dfrA14 is an integron-encoded dihydrofolate reductase found in Escherichia coli	diaminopyrimidine
contig00019	89658	90830	emrA	0/0	100.0	100.0	AP009048:2810082-2811255	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	fluoroquinolone
contig00019	90847	92385	emrB	0/0	100.0	100.0	U00096:2812615-2814154	emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin.	fluoroquinolone
contig00014	106777	107832	emrK	0/0	100.0	99.9	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00019	89001	89531	emrR	0/0	100.0	99.8	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00014	105239	106777	emrY	0/0	100.0	99.9	D78168:1591-3130	emrY is a multidrug transport that moves substrates across the inner membrane of the Gram-negative E. coli. It is a homolog of emrB.	tetracycline
contig00003	178034	179677	eptA	0/0	100.0	99.9	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00002	72967	74160	Escherichia_coli_acrA	0/0	100.0	100.0	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00003	134679	135812	Escherichia_coli_ampC	0/0	100.0	100.0	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00027	59	1363	Escherichia_coli_ampC1_beta-lactamase	0/0	100.0	100.0	FN649414.1:2765050-2766355	An ampC-like beta-lactamase identified from Escherichia coli.	cephalosporin, penam
contig00002	162299	163456	Escherichia_coli_ampH	0/0	100.0	100.0	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig00029	30138	31370	Escherichia_coli_mdfA	0/0	100.0	98.4	JQ394987:0-1233	Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter.	benzalkonium_chloride, rhodamine, tetracycline
contig00057	5607	6221	evgA	0/0	100.0	98.5	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00057	2009	5602	evgS	0/0	100.0	95.9	U00096:2484373-2487967	EvgS is a sensor protein that phosphorylates the regulatory protein EvgA. evgS corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	fluoroquinolone, macrolide, penam, tetracycline
contig00034	1784	2512	gadW	0/0	100.0	94.7	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig00034	592	1416	gadX	0/0	100.0	100.0	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00032	5379	5792	H-NS	0/0	100.0	99.3	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00012	8266	8943	kdpE	0/0	100.0	100.0	U00096.3:721733-721055	kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding.	aminoglycoside
contig00026	47772	48155	marA	0/0	100.0	100.0	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00025	29919	31166	mdtA	0/0	100.0	97.8	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00025	31166	34288	mdtB	0/0	100.0	97.7	U00096:2155262-2158385	MdtB is a transporter that forms a heteromultimer complex with MdtC to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex.	aminocoumarin
contig00025	34289	37366	mdtC	0/0	100.0	98.4	U00096:2158385-2161463	MdtC is a transporter that forms a heteromultimer complex with MdtB to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex. In the absence of MdtB MdtC can form a homomultimer complex that results in a functioning efflux complex with a narrower drug specificity. mdtC corresponds to 3 loci in Pseudomonas aeruginosa PAO1 (gene name: muxC/muxB) and 3 loci in Pseudomonas aeruginosa LESB58.	aminocoumarin
contig00034	6013	7170	mdtE	0/0	100.0	100.0	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00034	2875	5988	mdtF	0/0	100.0	100.0	U00096:3660413-3663527	MdtF is the multidrug inner membrane transporter for the MdtEF-TolC efflux complex.	fluoroquinolone, macrolide, penam
contig00007	18396	19622	mdtG	0/0	100.0	99.4	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00007	28251	29459	mdtH	0/0	100.0	99.9	U00096:1125326-1124117	Multidrug resistance protein MdtH	fluoroquinolone
contig00020	71909	73141	mdtM	0/0	100.0	96.2	U00096.3:4568519-4567286	Multidrug resistance protein MdtM	acridine_dye, fluoroquinolone, lincosamide, nucleoside, phenicol
contig00017	10879	11910	mdtN	0/0	100.0	100.0	AP009048.1:4307588-4306556	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	acridine_dye, nucleoside
contig00017	11910	13961	mdtO	0/0	100.0	100.0	AP009048.1:4306557-4304505	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00017	13958	15424	mdtP	0/0	100.0	100.0	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00005	129685	130161	mphB	0/0	100.0	98.3	AE005174.2:3397370-3397847	The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides.	macrolide
contig00006	51374	53122	msbA	0/0	100.0	100.0	U00096.3:966620-968369	MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability.	nitroimidazole
contig00014	1887	2855	pmrF	0/0	100.0	100.0	U00096:2367070-2368039	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide
contig00047	13875	14531	QnrS1	0/0	100.0	100.0	DQ485529.1:0-657	QnrS1 is a plasmid-mediated quinolone resistance protein found in Shigella flexneri	fluoroquinolone
contig00005	109476	110291	sul2	0/0	100.0	100.0	AY055428.1:21084-20268	Sul2 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria usually found on small plasmids.	sulfonamide
contig00047	3417	4277	TEM-1	0/0	100.0	99.9	AL513383:161910-162771	TEM-1 is a broad-spectrum beta-lactamase found in many Gram-negative bacteria. Confers resistance to penicillins and first generation cephalosphorins.	cephalosporin, monobactam, penam, penem
contig00047	835	2081	tet(A)	0/0	97.8	100.0	AF534183.1:2970-4245	TetA is a tetracycline efflux pump found in many species of Gram-negative bacteria.	tetracycline
contig00030	43942	45429	tolC	0/0	100.0	100.0	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan
contig00010	56579	58222	yojI	0/0	100.0	99.9	U00096.3:2308615-2306971	YojI mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. YojI is capable of pumping out microcin molecules. The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI.	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00027	59	1363	(Bla)AmpC1_Ecoli	0/0	100	100.0	FN649414:2765051-2766355	(Bla)AmpC1_Ecoli	NA
contig00003	134679	135812	(Bla)AmpC2_Ecoli	0/0	100	100.0	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00002	162299	163456	(Bla)ampH_Ecoli	0/0	100	100.0	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00047	8359	9234	(Bla)blaCTX-M-15	0/0	100	100.0	JQ686199:261-1136	(Bla)blaCTX-M-15	NA
contig00047	3417	4277	(Bla)blaTEM-105	0/0	100	99.9	AF516720:215-1075	(Bla)blaTEM-105	NA
contig00012	60354	62255	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100	100.0	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA
contig00047	13875	14531	(Flq)qnr-S1	0/0	100	100.0	AB187515:9737-10393	(Flq)qnr-S1	NA
contig00005	109476	110291	(Sul)sul2	0/0	100	100.0	EU360945:1617-2432	(Sul)sul2	NA
contig00047	835	2109	(Tet)tetA	0/0	100	100.0	JX424423:94438-95712	(Tet)tetA	NA
contig00047	154	804	(Tet)tetR	0/0	100	100.0	HF545434:53576-54226	(Tet)tetR	NA
contig00078	183	656	(Tmt)dfrA14	0/0	100	100.0	GU726917:72-545	(Tmt)dfrA14	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00047	8359	9234	blaCTX-M-15	0/0	100	100	NG_048935.1	class A extended-spectrum beta-lactamase CTX-M-15	CEPHALOSPORIN
contig00003	134679	135812	blaEC	0/0	100	100	NG_047494.1	BlaEC family class C beta-lactamase	BETA-LACTAM
contig00047	3417	4277	blaTEM-1	0/0	100	100	NG_050145.1	class A broad-spectrum beta-lactamase TEM-1	BETA-LACTAM
contig00078	183	656	dfrA14	0/0	100	100	NG_056035.1	trimethoprim-resistant dihydrofolate reductase DfrA14	TRIMETHOPRIM
contig00047	13875	14531	qnrS1	0/0	100	100	NG_050543.1	quinolone resistance pentapeptide repeat protein QnrS1	QUINOLONE
contig00005	109476	110291	sul2	0/0	100	100	NG_051852.1	sulfonamide-resistant dihydropteroate synthase Sul2	SULFONAMIDE
contig00047	910	2109	tet(A)	0/0	100	100	NG_048154.1	tetracycline efflux MFS transporter Tet(A)	TETRACYCLINE

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00002	72967	74160	ACRA	0/0	100.0	100.0	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00002	74183	77332	ACRB	0/0	100.0	100.0	MEG_401	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRB	NA
contig00005	150847	153960	ACRD	0/0	100.0	100.0	MEG_407	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ACRD	NA
contig00003	134679	135812	AMPC	0/0	100.0	100.0	MEG_728	Drugs:betalactams:Class_C_betalactamases:AMPC	NA
contig00002	162299	163456	AMPH	0/0	100.0	100.0	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00025	15659	17511	ASMA	0/0	100.0	96.9	MEG_1180	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:ASMA	NA
contig00023	65865	66686	BACA	0/0	100.0	100.0	MEG_1190	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00025	40179	40901	BAER	0/0	100.0	100.0	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00025	38779	40182	BAES	0/0	100.0	100.0	MEG_1193	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES	NA
contig00010	84009	85199	BCR	0/0	100.0	99.9	MEG_1210	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR	NA
contig00022	60628	61326	CPXAR	0/0	100.0	100.0	MEG_2122	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00022	61323	62696	CPXAR	0/0	100.0	100.0	MEG_2121	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00009	15261	15893	CRP	0/0	100.0	99.7	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00064	3523	4465	CTX	0/0	100.0	98.1	MEG_2435	Drugs:betalactams:Class_A_betalactamases:CTX	NA
contig00078	183	656	DFRA	0/0	100.0	99.8	MEG_2517	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00019	89658	90830	EMRA	0/0	100.0	100.0	MEG_2722	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA	NA
contig00019	90847	92385	EMRB	0/0	100.0	100.0	MEG_2725	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRB	NA
contig00011	75582	76772	EMRD	0/0	100.0	100.0	MEG_2729	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD	NA
contig00014	106777	107940	EMRK	0/0	100.0	99.9	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig00019	89001	89531	EMRR	0/0	100.0	99.8	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00014	105239	106777	EMRY	0/0	100.0	99.9	MEG_2736	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRY	NA
contig00003	178034	179677	EPTA	0/0	100.0	99.9	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig00057	2009	5602	EVGS	0/0	100.0	97.0	MEG_2869	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EVGS	NA
contig00034	1784	2512	GADW	0/0	100.0	100.0	MEG_3081	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig00034	592	1416	GADX	0/0	100.0	100.0	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00032	5379	5792	HNS	0/0	100.0	99.3	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00012	8266	8943	KDPE	0/0	100.0	100.0	MEG_3448	Drugs:Aminoglycosides:Aminoglycoside_efflux_pumps:KDPE	NA
contig00026	47766	48155	MARA	0/0	100.0	100.0	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00026	47318	47752	MARR	0/0	100.0	100.0	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00029	30138	31370	MDFA	0/0	100.0	99.9	MEG_3737	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDFA	NA
contig00025	29919	31166	MDTA	0/0	100.0	97.8	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00025	31166	34288	MDTB	0/0	100.0	97.7	MEG_3747	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTB	NA
contig00025	34289	37366	MDTC	0/0	100.0	98.4	MEG_3749	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTC	NA
contig00034	6013	7170	MDTE	0/0	100.0	100.0	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00034	2875	5988	MDTF	0/0	100.0	100.0	MEG_3752	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTF	NA
contig00007	18396	19622	MDTG	0/0	100.0	100.0	MEG_3753	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig00007	28251	29459	MDTH	0/0	100.0	99.9	MEG_3755	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTH	NA
contig00001	383533	383862	MDTI	0/0	100.0	100.0	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00001	383181	383546	MDTJ	0/0	100.0	99.5	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00001	311779	313152	MDTK	0/0	100.0	100.0	MEG_3759	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:MDTK	NA
contig00020	71909	73141	MDTM	0/0	100.0	96.2	MEG_3761	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTM	NA
contig00017	10879	11910	MDTN	0/0	100.0	100.0	MEG_3763	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN	NA
contig00017	11910	13961	MDTO	0/0	100.0	100.0	MEG_3764	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTO	NA
contig00017	13958	15424	MDTP	0/0	100.0	100.0	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig00005	129685	130161	MPHB	0/0	100.0	98.3	MEG_4033	Drugs:MLS:Macrolide_phosphotransferases:MPHB	NA
contig00006	51374	53122	MSBA	0/0	100.0	100.0	MEG_4061	Drugs:Multi-drug_resistance:Multi-drug_ABC_efflux_pumps:MSBA	NA
contig00012	60354	62255	PBP2	0/0	100.0	100.0	MEG_5400	Drugs:betalactams:Penicillin_binding_protein:PBP2	NA
contig00027	59	1363	PBP4B	0/0	100.0	100.0	MEG_5409	Drugs:betalactams:Penicillin_binding_protein:PBP4B	NA
contig00014	1887	2855	PMRF	0/0	100.0	100.0	MEG_5801	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF	NA
contig00047	13875	14531	QNRS	0/0	100.0	100.0	MEG_6020	Drugs:Fluoroquinolones:Quinolone_resistance_protein_Qnr:QNRS	NA
contig00020	11927	12796	ROBA	0/0	100.0	99.2	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00017	37040	37363	SOXS	0/0	100.0	100.0	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00005	109476	110291	SULII	0/0	100.0	100.0	MEG_6617	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULII	NA
contig00047	3399	4644	TEM	0/0	98.3	99.4	MEG_6875	Drugs:betalactams:Class_A_betalactamases:TEM	NA
contig00047	835	2109	TETA	0/0	100.0	100.0	MEG_7024	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETA	NA
contig00010	56579	58222	YOGI	0/0	100.0	99.9	MEG_7842	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:YOGI	NA

ID073I

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00078	1552	2355	aph(3’’)-Ib_5	0/0	100.0	100.0	AF321551	aph(3’’)-Ib	Streptomycin
contig00078	716	1552	aph(6)-Id_1	0/0	100.0	100.0	M28829	aph(6)-Id	Streptomycin
contig00059	11102	11977	blaCTX-M-15_1	0/0	100.0	100.0	AY044436	blaCTX-M-15	Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig00059	14798	15658	blaTEM-1B_1	0/0	100.0	100.0	AY458016	blaTEM-1B	Amoxicillin, Ampicillin, Cephalothin, Piperacillin, Ticarcillin
contig00094	179	661	dfrA14_5	0/0	100.0	99.6	DQ388123	dfrA14	Trimethoprim
contig00005	65535	66767	mdf(A)_1	0/0	100.0	99.3	Y08743	mdf(A)
contig00059	5805	6461	qnrS1_1	0/0	100.0	100.0	AB187515	qnrS1	Ciprofloxacin
contig00078	2416	3231	sul2_2	0/0	100.0	100.0	AY034138	sul2	Sulfamethoxazole
contig00059	16994	18240	tet(A)_6	0/0	97.8	100.0	AF534183	tet(A)	Doxycycline, Tetracycline

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00010	89518	92667	acrB	0/0	100.0	99.4	U00096.3:484403-481253	Protein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug/proton antiporter.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00001	135398	138511	acrD	0/0	100.0	99.3	AP009048.1:2586250-2589364	AcrD is an aminoglycoside efflux pump expressed in E. coli. Its expression can be induced by indole and is regulated by baeRS and cpxAR.	aminoglycoside
contig00006	140026	141183	acrE	0/0	100.0	99.0	U00096:3413863-3415021	AcrE is a membrane fusion protein similar to AcrA.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00006	141195	144299	acrF	0/0	100.0	99.0	U00096:3415032-3418137	AcrF is a inner membrane transporter similar to AcrB.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00006	138965	139627	acrS	0/0	100.0	99.1	U00096:3413465-3412802	AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.	cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00078	1552	2355	APH(3’’)-Ib	0/0	100.0	99.8	AF313472:15593-16397	APH(3’’)-Ib is an aminoglycoside phosphotransferase encoded by plasmids transposons integrative conjugative elements and chromosomes in Enterobacteriaceae and Pseudomonas spp.	aminoglycoside
contig00078	716	1552	APH(6)-Id	0/0	100.0	99.9	AF024602:3155-3992	APH(6)-Id is an aminoglycoside phosphotransferase encoded by plasmids integrative conjugative elements and chromosomal genomic islands in K. pneumoniae Salmonella spp. E. coli Shigella flexneri Providencia alcalifaciens Pseudomonas spp. V. cholerae Edwardsiella tarda Pasteurella multocida and Aeromonas bestiarum	aminoglycoside
contig00018	12213	13034	bacA	0/0	100.0	100.0	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00045	29538	30260	baeR	0/0	100.0	100.0	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00045	28138	29541	baeS	0/0	100.0	100.0	AP009048:2165012-2166416	BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.	aminocoumarin, aminoglycoside
contig00027	61701	63074	cpxA	0/0	100.0	98.7	BA000007.3:4905062-4903688	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	aminocoumarin, aminoglycoside
contig00013	15723	16355	CRP	0/0	100.0	99.4	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00059	11102	11977	CTX-M-15	0/0	100.0	100.0	AY044436:1435-2311	CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family	cephalosporin
contig00094	179	661	dfrA14	0/0	100.0	99.8	EU780012:2162-2645	dfrA14 is an integron-encoded dihydrofolate reductase found in Escherichia coli	diaminopyrimidine
contig00009	56609	57781	emrA	0/0	100.0	100.0	AP009048:2810082-2811255	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	fluoroquinolone
contig00009	57798	59336	emrB	0/0	100.0	100.0	U00096:2812615-2814154	emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin.	fluoroquinolone
contig00017	84975	86030	emrK	0/0	100.0	99.9	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00009	55952	56482	emrR	0/0	100.0	100.0	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00017	83437	84975	emrY	0/0	100.0	99.0	D78168:1591-3130	emrY is a multidrug transport that moves substrates across the inner membrane of the Gram-negative E. coli. It is a homolog of emrB.	tetracycline
contig00032	18804	20447	eptA	0/0	100.0	99.8	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00010	92690	93883	Escherichia_coli_acrA	0/0	100.0	100.0	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00007	131058	132191	Escherichia_coli_ampC	0/0	100.0	97.3	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00001	174991	176295	Escherichia_coli_ampC1_beta-lactamase	0/0	100.0	99.1	FN649414.1:2765050-2766355	An ampC-like beta-lactamase identified from Escherichia coli.	cephalosporin, penam
contig00010	3503	4660	Escherichia_coli_ampH	0/0	100.0	98.8	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig00048	30592	30924	Escherichia_coli_emrE	0/0	100.0	91.9	Z11877.1:485-818	Member of the small MDR (multidrug resistance) family of transporters, in Escherichia coli this protein provides resistance against a number of positively charged compounds including ethidium bromide and erythromycin, proton-dependent secondary transporter which exchanges protons for compound translocation	macrolide
contig00005	65535	66767	Escherichia_coli_mdfA	0/0	100.0	97.8	JQ394987:0-1233	Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter.	benzalkonium_chloride, rhodamine, tetracycline
contig00001	230782	234375	evgS	0/0	100.0	100.0	U00096:2484373-2487967	EvgS is a sensor protein that phosphorylates the regulatory protein EvgA. evgS corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	fluoroquinolone, macrolide, penam, tetracycline
contig00090	89	3682	evgS	0/0	100.0	95.9	U00096:2484373-2487967	EvgS is a sensor protein that phosphorylates the regulatory protein EvgA. evgS corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	fluoroquinolone, macrolide, penam, tetracycline
contig00026	31790	32518	gadW	0/0	100.0	94.7	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig00026	30598	31422	gadX	0/0	100.0	100.0	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00041	5323	5736	H-NS	0/0	100.0	99.0	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00036	43812	44489	kdpE	0/0	100.0	99.1	U00096.3:721733-721055	kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding.	aminoglycoside
contig00066	3021	3404	marA	0/0	100.0	100.0	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00045	19278	20525	mdtA	0/0	100.0	99.9	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00045	20525	23647	mdtB	0/0	100.0	99.8	U00096:2155262-2158385	MdtB is a transporter that forms a heteromultimer complex with MdtC to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex.	aminocoumarin
contig00045	23648	26725	mdtC	0/0	100.0	99.9	U00096:2158385-2161463	MdtC is a transporter that forms a heteromultimer complex with MdtB to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex. In the absence of MdtB MdtC can form a homomultimer complex that results in a functioning efflux complex with a narrower drug specificity. mdtC corresponds to 3 loci in Pseudomonas aeruginosa PAO1 (gene name: muxC/muxB) and 3 loci in Pseudomonas aeruginosa LESB58.	aminocoumarin
contig00026	36019	37176	mdtE	0/0	100.0	99.9	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00026	32881	35994	mdtF	0/0	100.0	100.0	U00096:3660413-3663527	MdtF is the multidrug inner membrane transporter for the MdtEF-TolC efflux complex.	fluoroquinolone, macrolide, penam
contig00056	2961	4187	mdtG	0/0	100.0	99.7	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00004	5672	6880	mdtH	0/0	100.0	98.4	U00096:1125326-1124117	Multidrug resistance protein MdtH	fluoroquinolone
contig00016	69851	71082	mdtM	1/1	99.9	96.2	U00096.3:4568519-4567286	Multidrug resistance protein MdtM	acridine_dye, fluoroquinolone, lincosamide, nucleoside, phenicol
contig00014	5198	6229	mdtN	0/0	100.0	100.0	AP009048.1:4307588-4306556	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	acridine_dye, nucleoside
contig00014	6229	8280	mdtO	0/0	100.0	99.1	AP009048.1:4306557-4304505	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00014	8277	9743	mdtP	0/0	100.0	100.0	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00001	114244	114720	mphB	0/0	100.0	98.3	AE005174.2:3397370-3397847	The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides.	macrolide
contig00002	125280	127028	msbA	0/0	100.0	100.0	U00096.3:966620-968369	MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability.	nitroimidazole
contig00021	15347	16315	pmrF	0/0	100.0	99.6	U00096:2367070-2368039	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide
contig00059	5805	6461	QnrS1	0/0	100.0	100.0	DQ485529.1:0-657	QnrS1 is a plasmid-mediated quinolone resistance protein found in Shigella flexneri	fluoroquinolone
contig00078	2416	3231	sul2	0/0	100.0	100.0	AY055428.1:21084-20268	Sul2 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria usually found on small plasmids.	sulfonamide
contig00059	14798	15658	TEM-1	0/0	100.0	99.9	AL513383:161910-162771	TEM-1 is a broad-spectrum beta-lactamase found in many Gram-negative bacteria. Confers resistance to penicillins and first generation cephalosphorins.	cephalosporin, monobactam, penam, penem
contig00059	16994	18240	tet(A)	0/0	97.8	100.0	AF534183.1:2970-4245	TetA is a tetracycline efflux pump found in many species of Gram-negative bacteria.	tetracycline
contig00024	60816	62303	tolC	0/0	100.0	99.7	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan
contig00021	74577	76220	yojI	0/0	100.0	99.7	U00096.3:2308615-2306971	YojI mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. YojI is capable of pumping out microcin molecules. The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI.	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00078	1552	2355	(AGly)strA	0/0	100	99.9	AB366441:22458-23261	(AGly)strA	NA
contig00078	716	1552	(AGly)strB	0/0	100	100.0	FJ474091:264-1100	(AGly)strB	NA
contig00001	174991	176295	(Bla)AmpC1_Ecoli	0/0	100	99.1	FN649414:2765051-2766355	(Bla)AmpC1_Ecoli	NA
contig00007	131058	132191	(Bla)AmpC2_Ecoli	0/0	100	97.3	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00010	3503	4660	(Bla)ampH_Ecoli	0/0	100	98.8	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00059	11102	11977	(Bla)blaCTX-M-15	0/0	100	100.0	JQ686199:261-1136	(Bla)blaCTX-M-15	NA
contig00059	14798	15658	(Bla)blaTEM-105	0/0	100	99.9	AF516720:215-1075	(Bla)blaTEM-105	NA
contig00015	34688	36589	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100	99.4	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA
contig00059	5805	6461	(Flq)qnr-S1	0/0	100	100.0	AB187515:9737-10393	(Flq)qnr-S1	NA
contig00078	2416	3231	(Sul)sul2	0/0	100	100.0	EU360945:1617-2432	(Sul)sul2	NA
contig00059	16966	18240	(Tet)tetA	0/0	100	100.0	JX424423:94438-95712	(Tet)tetA	NA
contig00094	179	652	(Tmt)dfrA14	0/0	100	100.0	GU726917:72-545	(Tmt)dfrA14	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00078	1552	2379	aph(3’’)-Ib	0/0	100	100.0	NG_056002.2	aminoglycoside O-phosphotransferase APH(3’’)-Ib	STREPTOMYCIN
contig00078	716	1552	aph(6)-Id	0/0	100	100.0	NG_047464.1	aminoglycoside O-phosphotransferase APH(6)-Id	STREPTOMYCIN
contig00059	11102	11977	blaCTX-M-15	0/0	100	100.0	NG_048935.1	class A extended-spectrum beta-lactamase CTX-M-15	CEPHALOSPORIN
contig00007	131058	132191	blaEC-15	0/0	100	98.6	NG_049081.1	class C extended-spectrum beta-lactamase EC-15	CEPHALOSPORIN
contig00059	14798	15658	blaTEM-1	0/0	100	100.0	NG_050145.1	class A broad-spectrum beta-lactamase TEM-1	BETA-LACTAM
contig00094	179	652	dfrA14	0/0	100	100.0	NG_056035.1	trimethoprim-resistant dihydrofolate reductase DfrA14	TRIMETHOPRIM
contig00059	5805	6461	qnrS1	0/0	100	100.0	NG_050543.1	quinolone resistance pentapeptide repeat protein QnrS1	QUINOLONE
contig00078	2416	3231	sul2	0/0	100	100.0	NG_051852.1	sulfonamide-resistant dihydropteroate synthase Sul2	SULFONAMIDE
contig00059	16966	18165	tet(A)	0/0	100	100.0	NG_048154.1	tetracycline efflux MFS transporter Tet(A)	TETRACYCLINE

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00010	92690	93883	ACRA	0/0	100.0	100.0	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00010	89518	92667	ACRB	0/0	100.0	99.4	MEG_401	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRB	NA
contig00001	135398	138511	ACRD	0/0	100.0	99.3	MEG_407	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ACRD	NA
contig00006	140026	141183	ACRE	0/0	100.0	99.0	MEG_408	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRE	NA
contig00006	141195	144299	ACRF	0/0	100.0	99.0	MEG_409	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRF	NA
contig00006	138965	139627	ACRS	0/0	100.0	99.1	MEG_415	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS	NA
contig00010	3503	4660	AMPH	0/0	100.0	98.8	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00078	1552	2379	APH3-DPRIME	0/0	100.0	100.0	MEG_1019	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH3-DPRIME	NA
contig00078	716	1552	APH6	0/0	100.0	100.0	MEG_1086	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH6	NA
contig00045	5081	6934	ASMA	0/0	100.0	96.9	MEG_1180	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:ASMA	NA
contig00018	12213	13034	BACA	0/0	100.0	100.0	MEG_1190	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00045	29538	30260	BAER	0/0	100.0	100.0	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00045	28138	29541	BAES	0/0	100.0	100.0	MEG_1193	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES	NA
contig00022	48987	50177	BCR	0/0	100.0	100.0	MEG_1210	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR	NA
contig00007	131058	132191	BLAEC	0/0	100.0	98.6	MEG_1282	Drugs:betalactams:Class_C_betalactamases:BLAEC	NA
contig00027	61006	61704	CPXAR	0/0	100.0	99.9	MEG_2118	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00027	61701	63074	CPXAR	0/0	100.0	99.4	MEG_2121	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00013	15723	16355	CRP	0/0	100.0	99.4	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00001	166242	167182	CTX	0/0	99.8	91.8	MEG_2435	Drugs:betalactams:Class_A_betalactamases:CTX	NA
contig00094	179	652	DFRA	0/0	100.0	99.8	MEG_2517	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00009	56609	57781	EMRA	0/0	100.0	100.0	MEG_2722	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA	NA
contig00009	57798	59336	EMRB	0/0	100.0	100.0	MEG_2725	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRB	NA
contig00060	14216	15406	EMRD	0/0	100.0	99.7	MEG_2729	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD	NA
contig00017	84975	86138	EMRK	0/0	100.0	99.9	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig00009	55952	56482	EMRR	0/0	100.0	100.0	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00017	83437	84975	EMRY	0/0	100.0	99.1	MEG_2736	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRY	NA
contig00032	18804	20447	EPTA	0/0	100.0	99.8	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig00001	230782	234375	EVGS	0/0	100.0	100.0	MEG_2870	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EVGS	NA
contig00090	89	3682	EVGS	0/0	100.0	97.0	MEG_2869	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EVGS	NA
contig00026	31790	32518	GADW	0/0	100.0	100.0	MEG_3081	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig00026	30598	31422	GADX	0/0	100.0	100.0	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00041	5323	5736	HNS	0/0	100.0	99.0	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00036	43812	44489	KDPE	0/0	100.0	99.1	MEG_3448	Drugs:Aminoglycosides:Aminoglycoside_efflux_pumps:KDPE	NA
contig00066	3015	3404	MARA	0/0	100.0	100.0	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00066	2567	3001	MARR	0/0	100.0	97.5	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00005	65535	66767	MDFA	0/0	100.0	99.4	MEG_3737	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDFA	NA
contig00045	19278	20525	MDTA	0/0	100.0	99.9	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00045	20525	23647	MDTB	0/0	100.0	99.8	MEG_3747	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTB	NA
contig00045	23648	26725	MDTC	0/0	100.0	99.9	MEG_3749	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTC	NA
contig00026	36019	37176	MDTE	0/0	100.0	99.9	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00026	32881	35994	MDTF	0/0	100.0	100.0	MEG_3752	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTF	NA
contig00056	2961	4187	MDTG	0/0	100.0	99.7	MEG_3754	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig00004	5672	6880	MDTH	0/0	100.0	98.4	MEG_3755	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTH	NA
contig00030	35419	35748	MDTI	0/0	100.0	100.0	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00030	35067	35432	MDTJ	0/0	100.0	99.5	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00028	34496	35869	MDTK	0/0	100.0	98.9	MEG_3759	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:MDTK	NA
contig00016	69851	71082	MDTM	1/1	99.9	96.2	MEG_3761	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTM	NA
contig00014	5198	6229	MDTN	0/0	100.0	100.0	MEG_3763	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN	NA
contig00014	6229	8280	MDTO	0/0	100.0	99.1	MEG_3764	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTO	NA
contig00014	8277	9743	MDTP	0/0	100.0	100.0	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig00001	114244	114720	MPHB	0/0	100.0	98.3	MEG_4033	Drugs:MLS:Macrolide_phosphotransferases:MPHB	NA
contig00002	125280	127028	MSBA	0/0	100.0	100.0	MEG_4061	Drugs:Multi-drug_resistance:Multi-drug_ABC_efflux_pumps:MSBA	NA
contig00048	30592	30924	MVRC	0/0	100.0	91.9	MEG_4103	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MVRC	NA
contig00015	34688	36589	PBP2	0/0	100.0	99.4	MEG_5400	Drugs:betalactams:Penicillin_binding_protein:PBP2	NA
contig00001	174991	176295	PBP4B	0/0	100.0	99.1	MEG_5409	Drugs:betalactams:Penicillin_binding_protein:PBP4B	NA
contig00021	15347	16315	PMRF	0/0	100.0	99.6	MEG_5801	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF	NA
contig00059	5805	6461	QNRS	0/0	100.0	100.0	MEG_6020	Drugs:Fluoroquinolones:Quinolone_resistance_protein_Qnr:QNRS	NA
contig00016	21727	22596	ROBA	0/0	100.0	99.0	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00014	31811	32133	SOXS	0/0	99.7	99.7	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00078	2416	3231	SULII	0/0	100.0	100.0	MEG_6617	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULII	NA
contig00059	14431	15676	TEM	0/0	98.3	99.4	MEG_6875	Drugs:betalactams:Class_A_betalactamases:TEM	NA
contig00059	16966	18240	TETA	0/0	100.0	100.0	MEG_7024	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETA	NA
contig00021	74577	76220	YOGI	0/0	100.0	99.7	MEG_7842	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:YOGI	NA

ID077

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00051	1409	2212	aph(3’’)-Ib_5	0/0	100.0	100.0	AF321551	aph(3’’)-Ib	Streptomycin
contig00051	573	1409	aph(6)-Id_1	0/0	100.0	100.0	M28829	aph(6)-Id	Streptomycin
contig00044	1838	2713	blaCTX-M-15_1	0/0	100.0	100.0	AY044436	blaCTX-M-15	Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig00047	6403	7263	blaTEM-1B_1	0/0	100.0	100.0	AY458016	blaTEM-1B	Amoxicillin, Ampicillin, Cephalothin, Piperacillin, Ticarcillin
contig00057	182	664	dfrA14_5	0/0	100.0	99.6	DQ388123	dfrA14	Trimethoprim
contig00022	64602	65834	mdf(A)_1	0/0	100.0	99.1	Y08743	mdf(A)
contig00047	1	916	mph(A)_2	1/1	99.3	99.7	U36578	mph(A)	Erythromycin, Azithromycin, Spiramycin, Telithromycin
contig00044	7354	8010	qnrS1_1	0/0	100.0	100.0	AB187515	qnrS1	Ciprofloxacin
contig00051	2273	3088	sul2_2	0/0	100.0	100.0	AY034138	sul2	Sulfamethoxazole
contig00053	1676	2922	tet(A)_6	0/0	97.8	100.0	AF534183	tet(A)	Doxycycline, Tetracycline

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00012	124682	127831	acrB	0/0	100.0	99.1	U00096.3:484403-481253	Protein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug/proton antiporter.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00010	117709	120822	acrD	0/0	100.0	98.8	AP009048.1:2586250-2589364	AcrD is an aminoglycoside efflux pump expressed in E. coli. Its expression can be induced by indole and is regulated by baeRS and cpxAR.	aminoglycoside
contig00020	85157	86314	acrE	0/0	100.0	98.9	U00096:3413863-3415021	AcrE is a membrane fusion protein similar to AcrA.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00020	86326	89430	acrF	0/0	100.0	99.0	U00096:3415032-3418137	AcrF is a inner membrane transporter similar to AcrB.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00020	84096	84758	acrS	0/0	100.0	98.6	U00096:3413465-3412802	AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.	cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00051	1409	2212	APH(3’’)-Ib	0/0	100.0	99.8	AF313472:15593-16397	APH(3’’)-Ib is an aminoglycoside phosphotransferase encoded by plasmids transposons integrative conjugative elements and chromosomes in Enterobacteriaceae and Pseudomonas spp.	aminoglycoside
contig00051	573	1409	APH(6)-Id	0/0	100.0	99.9	AF024602:3155-3992	APH(6)-Id is an aminoglycoside phosphotransferase encoded by plasmids integrative conjugative elements and chromosomal genomic islands in K. pneumoniae Salmonella spp. E. coli Shigella flexneri Providencia alcalifaciens Pseudomonas spp. V. cholerae Edwardsiella tarda Pasteurella multocida and Aeromonas bestiarum	aminoglycoside
contig00007	60021	60840	bacA	0/0	99.8	98.7	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00014	115493	116215	baeR	0/0	100.0	99.5	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00014	114093	115496	baeS	0/0	100.0	98.7	AP009048:2165012-2166416	BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.	aminocoumarin, aminoglycoside
contig00030	22613	23986	cpxA	0/0	100.0	98.5	BA000007.3:4905062-4903688	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	aminocoumarin, aminoglycoside
contig00005	15000	15632	CRP	0/0	100.0	99.2	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00044	1838	2713	CTX-M-15	0/0	100.0	100.0	AY044436:1435-2311	CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family	cephalosporin
contig00057	182	664	dfrA14	0/0	100.0	99.8	EU780012:2162-2645	dfrA14 is an integron-encoded dihydrofolate reductase found in Escherichia coli	diaminopyrimidine
contig00025	57060	58232	emrA	0/0	100.0	98.2	AP009048:2810082-2811255	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	fluoroquinolone
contig00025	58249	59787	emrB	0/0	100.0	98.5	U00096:2812615-2814154	emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin.	fluoroquinolone
contig00010	25955	27010	emrK	0/0	100.0	98.7	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00025	56403	56933	emrR	0/0	100.0	100.0	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00010	24417	25955	emrY	0/0	100.0	98.8	D78168:1591-3130	emrY is a multidrug transport that moves substrates across the inner membrane of the Gram-negative E. coli. It is a homolog of emrB.	tetracycline
contig00027	18412	20055	eptA	0/0	100.0	99.2	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00012	127854	129047	Escherichia_coli_acrA	0/0	100.0	99.8	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00017	92232	93365	Escherichia_coli_ampC	0/0	100.0	97.2	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00010	85287	86591	Escherichia_coli_ampC1_beta-lactamase	0/0	100.0	98.2	FN649414.1:2765050-2766355	An ampC-like beta-lactamase identified from Escherichia coli.	cephalosporin, penam
contig00012	36338	37495	Escherichia_coli_ampH	0/0	100.0	98.7	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig00034	3107	3439	Escherichia_coli_emrE	0/0	100.0	92.5	Z11877.1:485-818	Member of the small MDR (multidrug resistance) family of transporters, in Escherichia coli this protein provides resistance against a number of positively charged compounds including ethidium bromide and erythromycin, proton-dependent secondary transporter which exchanges protons for compound translocation	macrolide
contig00022	64602	65834	Escherichia_coli_mdfA	0/0	100.0	97.6	JQ394987:0-1233	Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter.	benzalkonium_chloride, rhodamine, tetracycline
contig00010	27534	28148	evgA	0/0	100.0	99.0	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00010	28153	31746	evgS	0/0	100.0	99.5	U00096:2484373-2487967	EvgS is a sensor protein that phosphorylates the regulatory protein EvgA. evgS corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	fluoroquinolone, macrolide, penam, tetracycline
contig00005	190046	190774	gadW	0/0	100.0	94.4	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig00005	191142	191966	gadX	0/0	100.0	97.8	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00004	201604	202017	H-NS	0/0	100.0	99.3	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00006	8189	8861	kdpE	0/0	99.3	97.2	U00096.3:721733-721055	kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding.	aminoglycoside
contig00009	119325	119708	marA	0/0	100.0	99.5	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00014	105233	106480	mdtA	0/0	100.0	98.2	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00014	106480	109602	mdtB	0/0	100.0	98.0	U00096:2155262-2158385	MdtB is a transporter that forms a heteromultimer complex with MdtC to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex.	aminocoumarin
contig00014	109603	112680	mdtC	0/0	100.0	98.1	U00096:2158385-2161463	MdtC is a transporter that forms a heteromultimer complex with MdtB to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex. In the absence of MdtB MdtC can form a homomultimer complex that results in a functioning efflux complex with a narrower drug specificity. mdtC corresponds to 3 loci in Pseudomonas aeruginosa PAO1 (gene name: muxC/muxB) and 3 loci in Pseudomonas aeruginosa LESB58.	aminocoumarin
contig00005	185388	186545	mdtE	0/0	100.0	99.7	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00005	186570	189683	mdtF	0/0	100.0	98.6	U00096:3660413-3663527	MdtF is the multidrug inner membrane transporter for the MdtEF-TolC efflux complex.	fluoroquinolone, macrolide, penam
contig00003	188462	189688	mdtG	0/0	100.0	99.2	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00003	198319	199527	mdtH	0/0	100.0	98.8	U00096:1125326-1124117	Multidrug resistance protein MdtH	fluoroquinolone
contig00016	82731	83963	mdtM	0/0	100.0	95.9	U00096.3:4568519-4567286	Multidrug resistance protein MdtM	acridine_dye, fluoroquinolone, lincosamide, nucleoside, phenicol
contig00019	4218	5249	mdtN	0/0	100.0	98.0	AP009048.1:4307588-4306556	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	acridine_dye, nucleoside
contig00019	5249	7300	mdtO	0/0	100.0	98.7	AP009048.1:4306557-4304505	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00019	7297	8763	mdtP	0/0	100.0	98.2	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00047	11	916	mphA	0/0	100.0	100.0	D16251.1:2531-1625	The mphA gene encodes for resistance enzyme MPH(2’)-I which preferentially inactivate 14-membered macrolides (e.g.erythromycin telithromycin roxithromycin) over 16-membered macrolides (e.g.tylosin spiramycin). It phosphorylates macrolides at 2’-OH hydroxyl of desosamine sugar of macrolides in a GTP-dependent manner.	macrolide
contig00010	142312	142788	mphB	0/0	100.0	98.3	AE005174.2:3397370-3397847	The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides.	macrolide
contig00003	51626	53374	msbA	0/0	100.0	99.0	U00096.3:966620-968369	MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability.	nitroimidazole
contig00013	52356	53324	pmrF	0/0	100.0	99.4	U00096:2367070-2368039	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide
contig00044	7354	8010	QnrS1	0/0	100.0	100.0	DQ485529.1:0-657	QnrS1 is a plasmid-mediated quinolone resistance protein found in Shigella flexneri	fluoroquinolone
contig00051	2273	3088	sul2	0/0	100.0	100.0	AY055428.1:21084-20268	Sul2 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria usually found on small plasmids.	sulfonamide
contig00047	6403	7263	TEM-1	0/0	100.0	99.9	AL513383:161910-162771	TEM-1 is a broad-spectrum beta-lactamase found in many Gram-negative bacteria. Confers resistance to penicillins and first generation cephalosphorins.	cephalosporin, monobactam, penam, penem
contig00053	1676	2922	tet(A)	0/0	97.8	100.0	AF534183.1:2970-4245	TetA is a tetracycline efflux pump found in many species of Gram-negative bacteria.	tetracycline
contig00007	36175	37662	tolC	0/0	100.0	98.4	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan
contig00013	3695	5338	yojI	0/0	100.0	98.2	U00096.3:2308615-2306971	YojI mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. YojI is capable of pumping out microcin molecules. The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI.	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00051	1409	2212	(AGly)strA	0/0	100	99.9	AB366441:22458-23261	(AGly)strA	NA
contig00051	573	1409	(AGly)strB	0/0	100	100.0	FJ474091:264-1100	(AGly)strB	NA
contig00010	85287	86591	(Bla)AmpC1_Ecoli	0/0	100	98.2	FN649414:2765051-2766355	(Bla)AmpC1_Ecoli	NA
contig00017	92232	93365	(Bla)AmpC2_Ecoli	0/0	100	97.2	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00012	36338	37495	(Bla)ampH_Ecoli	0/0	100	98.7	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00044	1838	2713	(Bla)blaCTX-M-15	0/0	100	100.0	JQ686199:261-1136	(Bla)blaCTX-M-15	NA
contig00047	6403	7263	(Bla)blaTEM-105	0/0	100	99.9	AF516720:215-1075	(Bla)blaTEM-105	NA
contig00006	60650	62551	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100	98.7	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA
contig00044	7354	8010	(Flq)qnr-S1	0/0	100	100.0	AB187515:9737-10393	(Flq)qnr-S1	NA
contig00047	11	916	(MLS)mph(A)	0/0	100	100.0	DQ445270:1626-2531	(MLS)mph(A)	NA
contig00051	2273	3088	(Sul)sul2	0/0	100	100.0	EU360945:1617-2432	(Sul)sul2	NA
contig00053	1648	2922	(Tet)tetA	0/0	100	100.0	JX424423:94438-95712	(Tet)tetA	NA
contig00057	182	655	(Tmt)dfrA14	0/0	100	100.0	GU726917:72-545	(Tmt)dfrA14	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00051	1409	2236	aph(3’’)-Ib	0/0	100.0	100.0	NG_056002.2	aminoglycoside O-phosphotransferase APH(3’’)-Ib	STREPTOMYCIN
contig00051	573	1409	aph(6)-Id	0/0	100.0	100.0	NG_047464.1	aminoglycoside O-phosphotransferase APH(6)-Id	STREPTOMYCIN
contig00044	1838	2713	blaCTX-M-15	0/0	100.0	100.0	NG_048935.1	class A extended-spectrum beta-lactamase CTX-M-15	CEPHALOSPORIN
contig00017	92232	93365	blaEC-13	0/0	100.0	99.6	NG_049079.1	class C extended-spectrum beta-lactamase EC-13	CEPHALOSPORIN
contig00047	6403	7263	blaTEM-1	0/0	100.0	100.0	NG_050145.1	class A broad-spectrum beta-lactamase TEM-1	BETA-LACTAM
contig00057	182	655	dfrA14	0/0	100.0	100.0	NG_056035.1	trimethoprim-resistant dihydrofolate reductase DfrA14	TRIMETHOPRIM
contig00047	1	916	mph(A)	1/1	99.3	99.7	NG_047986.1	Mph(A) family macrolide 2’-phosphotransferase	MACROLIDE
contig00044	7354	8010	qnrS1	0/0	100.0	100.0	NG_050543.1	quinolone resistance pentapeptide repeat protein QnrS1	QUINOLONE
contig00051	2273	3088	sul2	0/0	100.0	100.0	NG_051852.1	sulfonamide-resistant dihydropteroate synthase Sul2	SULFONAMIDE
contig00053	1648	2847	tet(A)	0/0	100.0	100.0	NG_048154.1	tetracycline efflux MFS transporter Tet(A)	TETRACYCLINE

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00012	127854	129047	ACRA	0/0	100.0	99.8	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00012	124682	127831	ACRB	0/0	100.0	99.1	MEG_401	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRB	NA
contig00010	117709	120822	ACRD	0/0	100.0	98.8	MEG_407	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ACRD	NA
contig00020	85157	86314	ACRE	0/0	100.0	98.9	MEG_408	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRE	NA
contig00020	86326	89430	ACRF	0/0	100.0	99.0	MEG_409	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRF	NA
contig00020	84096	84758	ACRS	0/0	100.0	98.6	MEG_415	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS	NA
contig00012	36338	37495	AMPH	0/0	100.0	98.7	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00051	1409	2236	APH3-DPRIME	0/0	100.0	100.0	MEG_1019	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH3-DPRIME	NA
contig00051	573	1409	APH6	0/0	100.0	100.0	MEG_1086	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH6	NA
contig00014	90978	92830	ASMA	0/0	100.0	98.0	MEG_1180	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:ASMA	NA
contig00007	60021	60840	BACA	0/0	99.8	98.9	MEG_1189	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00014	115493	116215	BAER	0/0	100.0	99.5	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00014	114093	115496	BAES	0/0	100.0	98.7	MEG_1193	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES	NA
contig00024	21479	22669	BCR	0/0	100.0	98.2	MEG_1210	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR	NA
contig00017	92232	93365	BLAEC	0/0	100.0	99.6	MEG_1280	Drugs:betalactams:Class_C_betalactamases:BLAEC	NA
contig00030	21918	22616	CPXAR	0/0	100.0	99.4	MEG_2118	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00030	22613	23986	CPXAR	0/0	100.0	99.1	MEG_2121	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00005	15000	15632	CRP	0/0	100.0	99.2	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00057	182	655	DFRA	0/0	100.0	99.8	MEG_2517	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00025	57060	58232	EMRA	0/0	100.0	98.2	MEG_2722	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA	NA
contig00025	58249	59787	EMRB	0/0	100.0	98.5	MEG_2725	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRB	NA
contig00008	92225	93415	EMRD	0/0	100.0	99.9	MEG_2729	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD	NA
contig00010	25955	27118	EMRK	0/0	100.0	98.8	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig00025	56403	56933	EMRR	0/0	100.0	100.0	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00010	24417	25955	EMRY	0/0	100.0	98.9	MEG_2736	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRY	NA
contig00027	18412	20055	EPTA	0/0	100.0	99.2	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig00010	28153	31746	EVGS	0/0	100.0	99.5	MEG_2870	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EVGS	NA
contig00005	190046	190774	GADW	0/0	100.0	98.6	MEG_3081	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig00005	191142	191966	GADX	0/0	100.0	97.8	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00004	201604	202017	HNS	0/0	100.0	99.3	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00006	8189	8861	KDPE	0/0	99.3	97.2	MEG_3448	Drugs:Aminoglycosides:Aminoglycoside_efflux_pumps:KDPE	NA
contig00009	119325	119714	MARA	0/0	100.0	99.5	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00009	119728	120162	MARR	0/0	100.0	97.7	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00022	64602	65834	MDFA	0/0	100.0	99.2	MEG_3737	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDFA	NA
contig00014	105233	106480	MDTA	0/0	100.0	98.2	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00014	106480	109602	MDTB	0/0	100.0	98.0	MEG_3747	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTB	NA
contig00014	109603	112680	MDTC	0/0	100.0	98.1	MEG_3749	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTC	NA
contig00005	185388	186545	MDTE	0/0	100.0	99.7	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00005	186570	189683	MDTF	0/0	100.0	98.6	MEG_3752	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTF	NA
contig00003	188462	189688	MDTG	0/0	100.0	99.3	MEG_3753	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig00003	198319	199527	MDTH	0/0	100.0	98.8	MEG_3755	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTH	NA
contig00009	35311	35640	MDTI	0/0	100.0	99.7	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00009	34959	35324	MDTJ	0/0	100.0	98.9	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00002	34530	35903	MDTK	0/0	100.0	99.0	MEG_3759	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:MDTK	NA
contig00016	82731	83963	MDTM	0/0	100.0	95.9	MEG_3761	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTM	NA
contig00019	4218	5249	MDTN	0/0	100.0	98.0	MEG_3763	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN	NA
contig00019	5249	7300	MDTO	0/0	100.0	98.7	MEG_3764	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTO	NA
contig00019	7297	8763	MDTP	0/0	100.0	98.2	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig00047	1	916	MPHA	1/1	99.3	99.7	MEG_4030	Drugs:MLS:Macrolide_phosphotransferases:MPHA	NA
contig00010	142312	142788	MPHB	0/0	100.0	98.3	MEG_4033	Drugs:MLS:Macrolide_phosphotransferases:MPHB	NA
contig00003	51626	53374	MSBA	0/0	100.0	99.0	MEG_4061	Drugs:Multi-drug_resistance:Multi-drug_ABC_efflux_pumps:MSBA	NA
contig00034	3107	3439	MVRC	0/0	100.0	92.5	MEG_4103	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MVRC	NA
contig00006	60650	62551	PBP2	0/0	100.0	98.7	MEG_5400	Drugs:betalactams:Penicillin_binding_protein:PBP2	NA
contig00010	85287	86591	PBP4B	0/0	100.0	98.2	MEG_5409	Drugs:betalactams:Penicillin_binding_protein:PBP4B	NA
contig00013	52356	53324	PMRF	0/0	100.0	99.4	MEG_5801	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF	NA
contig00044	7354	8010	QNRS	0/0	100.0	100.0	MEG_6020	Drugs:Fluoroquinolones:Quinolone_resistance_protein_Qnr:QNRS	NA
contig00016	11978	12847	ROBA	0/0	100.0	99.1	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00019	30380	30703	SOXS	0/0	100.0	100.0	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00051	2273	3088	SULII	0/0	100.0	100.0	MEG_6617	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULII	NA
contig00047	6385	7630	TEM	0/0	98.3	99.4	MEG_6875	Drugs:betalactams:Class_A_betalactamases:TEM	NA
contig00053	1648	2922	TETA	0/0	100.0	100.0	MEG_7024	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETA	NA
contig00013	3695	5338	YOGI	0/0	100.0	98.2	MEG_7842	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:YOGI	NA

ID081I

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00103	1585	2388	aph(3’’)-Ib_5	0/0	100.0	100.0	AF321551	aph(3’’)-Ib	Streptomycin
contig00103	749	1585	aph(6)-Id_1	0/0	100.0	100.0	M28829	aph(6)-Id	Streptomycin
contig00036	35508	36383	blaCTX-M-55_1	0/0	100.0	100.0	DQ810789	blaCTX-M-55	Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig00075	1306	2445	blaDHA-1_1	0/0	100.0	100.0	Y16410	blaDHA-1	Amoxicillin, Amoxicillin+Clavulanic_acid, Ampicillin, Ampicillin+Clavulanic_acid, Cefotaxime, Cefoxitin, Ceftazidime, Piperacillin, Piperacillin+Tazobactam, Ticarcillin, Ticarcillin+Clavulanic_acid
contig00064	9630	10490	blaTEM-1B_1	0/0	100.0	100.0	AY458016	blaTEM-1B	Amoxicillin, Ampicillin, Cephalothin, Piperacillin, Ticarcillin
contig00177	182	664	dfrA14_5	0/0	100.0	99.6	DQ388123	dfrA14	Trimethoprim
contig00158	460	933	dfrA17_1	0/0	100.0	100.0	FJ460238	dfrA17	Trimethoprim
contig00125	200	773	dfrA7_5	3/4	100.0	98.8	AJ419170	dfrA7	Trimethoprim
contig00117	262	1025	erm(B)_18	2/2	100.0	99.0	X66468	erm(B)	Erythromycin, Lincomycin, Clindamycin, Quinupristin, Pristinamycin_IA, Virginiamycin_S
contig00011	56271	57503	mdf(A)_1	0/0	100.0	99.9	Y08743	mdf(A)
contig00162	1	882	mph(A)_1	0/0	97.3	100.0	D16251	mph(A)	Erythromycin, Azithromycin, Spiramycin, Telithromycin
contig00075	6569	7213	qnrB4_1	0/0	100.0	100.0	DQ303921	qnrB4	Ciprofloxacin
contig00064	3612	4268	qnrS1_1	0/0	100.0	100.0	AB187515	qnrS1	Ciprofloxacin
contig00082	223	1089	sul1_5	0/0	100.0	99.9	EU780013	sul1	Sulfamethoxazole
contig00103	2449	3264	sul2_2	0/0	100.0	100.0	AY034138	sul2	Sulfamethoxazole
contig00064	11826	13072	tet(A)_6	0/0	97.8	100.0	AF534183	tet(A)	Doxycycline, Tetracycline

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00003	133793	136942	acrB	0/0	100.0	99.5	U00096.3:484403-481253	Protein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug/proton antiporter.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00013	15665	18778	acrD	0/0	100.0	98.9	AP009048.1:2586250-2589364	AcrD is an aminoglycoside efflux pump expressed in E. coli. Its expression can be induced by indole and is regulated by baeRS and cpxAR.	aminoglycoside
contig00044	8641	9798	acrE	0/0	100.0	98.9	U00096:3413863-3415021	AcrE is a membrane fusion protein similar to AcrA.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00044	5525	8629	acrF	0/0	100.0	99.0	U00096:3415032-3418137	AcrF is a inner membrane transporter similar to AcrB.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00044	10197	10859	acrS	0/0	100.0	99.1	U00096:3413465-3412802	AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.	cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00103	1585	2388	APH(3’’)-Ib	0/0	100.0	99.8	AF313472:15593-16397	APH(3’’)-Ib is an aminoglycoside phosphotransferase encoded by plasmids transposons integrative conjugative elements and chromosomes in Enterobacteriaceae and Pseudomonas spp.	aminoglycoside
contig00103	749	1585	APH(6)-Id	0/0	100.0	99.9	AF024602:3155-3992	APH(6)-Id is an aminoglycoside phosphotransferase encoded by plasmids integrative conjugative elements and chromosomal genomic islands in K. pneumoniae Salmonella spp. E. coli Shigella flexneri Providencia alcalifaciens Pseudomonas spp. V. cholerae Edwardsiella tarda Pasteurella multocida and Aeromonas bestiarum	aminoglycoside
contig00001	301816	302637	bacA	0/0	100.0	100.0	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00027	9118	9840	baeR	0/0	100.0	97.8	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00027	9837	11240	baeS	0/0	100.0	99.3	AP009048:2165012-2166416	BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.	aminocoumarin, aminoglycoside
contig00026	22842	24215	cpxA	0/0	100.0	98.0	BA000007.3:4905062-4903688	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	aminocoumarin, aminoglycoside
contig00010	14930	15562	CRP	0/0	100.0	99.4	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00036	35508	36383	CTX-M-55	0/0	100.0	100.0	DQ885477:0-876	CTX-M-55 is a beta-lactamase found in the Enterobacteriaceae family	cephalosporin
contig00177	182	664	dfrA14	0/0	100.0	99.8	EU780012:2162-2645	dfrA14 is an integron-encoded dihydrofolate reductase found in Escherichia coli	diaminopyrimidine
contig00158	460	933	dfrA17	0/0	100.0	100.0	DQ838665:0-474	dfrA17 is an integron-encoded dihydrofolate reductase found in Escherichia coli	diaminopyrimidine
contig00125	300	773	dfrA7	0/0	100.0	100.0	FJ854362:2338-2812	dfrA7 is an integron-encoded dihydrofolate reductase found in Escherichia coli	diaminopyrimidine
contig00075	1306	2445	DHA-1	0/0	100.0	100.0	Y16410.1:986-2126	DHA-1 is a class C beta-lactamase found in Morganella morganii and Salmonella enterica	cephalosporin, cephamycin
contig00016	26008	27180	emrA	0/0	100.0	98.1	AP009048:2810082-2811255	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	fluoroquinolone
contig00016	27197	28735	emrB	0/0	100.0	99.3	U00096:2812615-2814154	emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin.	fluoroquinolone
contig00058	16778	17833	emrK	0/0	100.0	99.9	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00016	25351	25881	emrR	0/0	100.0	100.0	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00058	15240	16778	emrY	0/0	100.0	99.0	D78168:1591-3130	emrY is a multidrug transport that moves substrates across the inner membrane of the Gram-negative E. coli. It is a homolog of emrB.	tetracycline
contig00052	1560	3203	eptA	0/0	100.0	99.8	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00117	288	1033	ErmB	1/1	99.9	99.2	AF242872.1:2131-2878	ErmB confers the MLSb phenotype. Similar to ErmC expression of ErmB is inducible by erythromycin. The leader peptide causes attenuation of the mRNA and stabilizes the structure preventing further translation. When erythromycin is present it binds the leader peptide causing a change in conformation allowing for the expression of ErmB.	lincosamide, macrolide, streptogramin
contig00003	136965	138158	Escherichia_coli_acrA	0/0	100.0	99.8	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00019	48520	49653	Escherichia_coli_ampC	0/0	100.0	97.3	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00013	50176	51480	Escherichia_coli_ampC1_beta-lactamase	0/0	100.0	99.4	FN649414.1:2765050-2766355	An ampC-like beta-lactamase identified from Escherichia coli.	cephalosporin, penam
contig00003	47670	48827	Escherichia_coli_ampH	0/0	100.0	98.9	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig00104	2538	2870	Escherichia_coli_emrE	0/0	100.0	91.9	Z11877.1:485-818	Member of the small MDR (multidrug resistance) family of transporters, in Escherichia coli this protein provides resistance against a number of positively charged compounds including ethidium bromide and erythromycin, proton-dependent secondary transporter which exchanges protons for compound translocation	macrolide
contig00011	56271	57503	Escherichia_coli_mdfA	0/0	100.0	98.4	JQ394987:0-1233	Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter.	benzalkonium_chloride, rhodamine, tetracycline
contig00013	110122	113715	evgS	0/0	100.0	100.0	U00096:2484373-2487967	EvgS is a sensor protein that phosphorylates the regulatory protein EvgA. evgS corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	fluoroquinolone, macrolide, penam, tetracycline
contig00045	2243	2971	gadW	0/0	100.0	94.4	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig00045	1051	1875	gadX	0/0	100.0	97.7	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00017	22891	23304	H-NS	0/0	100.0	99.5	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00002	95589	96266	kdpE	0/0	100.0	99.3	U00096.3:721733-721055	kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding.	aminoglycoside
contig00039	13399	13782	marA	0/0	100.0	99.2	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00027	18853	20100	mdtA	0/0	100.0	97.2	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00027	15731	18853	mdtB	0/0	100.0	96.9	U00096:2155262-2158385	MdtB is a transporter that forms a heteromultimer complex with MdtC to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex.	aminocoumarin
contig00027	12653	15730	mdtC	0/0	100.0	97.6	U00096:2158385-2161463	MdtC is a transporter that forms a heteromultimer complex with MdtB to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex. In the absence of MdtB MdtC can form a homomultimer complex that results in a functioning efflux complex with a narrower drug specificity. mdtC corresponds to 3 loci in Pseudomonas aeruginosa PAO1 (gene name: muxC/muxB) and 3 loci in Pseudomonas aeruginosa LESB58.	aminocoumarin
contig00045	6472	7629	mdtE	0/0	100.0	99.7	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00045	3334	6447	mdtF	0/0	100.0	98.5	U00096:3660413-3663527	MdtF is the multidrug inner membrane transporter for the MdtEF-TolC efflux complex.	fluoroquinolone, macrolide, penam
contig00022	72668	73894	mdtG	0/0	100.0	99.4	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00022	62829	64037	mdtH	0/0	100.0	97.9	U00096:1125326-1124117	Multidrug resistance protein MdtH	fluoroquinolone
contig00020	77	1108	mdtN	0/0	100.0	100.0	AP009048.1:4307588-4306556	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	acridine_dye, nucleoside
contig00020	1108	3159	mdtO	0/0	100.0	99.1	AP009048.1:4306557-4304505	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00020	3156	4622	mdtP	0/0	100.0	99.9	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00162	1	882	mphA	0/0	97.3	100.0	D16251.1:2531-1625	The mphA gene encodes for resistance enzyme MPH(2’)-I which preferentially inactivate 14-membered macrolides (e.g.erythromycin telithromycin roxithromycin) over 16-membered macrolides (e.g.tylosin spiramycin). It phosphorylates macrolides at 2’-OH hydroxyl of desosamine sugar of macrolides in a GTP-dependent manner.	macrolide
contig00012	5046	5522	mphB	0/0	100.0	98.1	AE005174.2:3397370-3397847	The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides.	macrolide
contig00009	71622	73370	msbA	0/0	100.0	100.0	U00096.3:966620-968369	MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability.	nitroimidazole
contig00004	102028	102996	pmrF	0/0	100.0	99.6	U00096:2367070-2368039	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide
contig00075	6566	7213	QnrB4	0/0	100.0	100.0	DQ303921:0-648	QnrB4 is a plasmid-mediated quinolone resistance protein found in Escherichia coli	fluoroquinolone
contig00064	3612	4268	QnrS1	0/0	100.0	100.0	DQ485529.1:0-657	QnrS1 is a plasmid-mediated quinolone resistance protein found in Shigella flexneri	fluoroquinolone
contig00082	250	1089	sul1	0/0	100.0	100.0	JF969163:1053-1893	Sul1 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria. It is linked to other resistance genes of class 1 integrons.	sulfonamide
contig00103	2449	3264	sul2	0/0	100.0	100.0	AY055428.1:21084-20268	Sul2 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria usually found on small plasmids.	sulfonamide
contig00064	9630	10490	TEM-1	0/0	100.0	99.9	AL513383:161910-162771	TEM-1 is a broad-spectrum beta-lactamase found in many Gram-negative bacteria. Confers resistance to penicillins and first generation cephalosphorins.	cephalosporin, monobactam, penam, penem
contig00064	11826	13072	tet(A)	0/0	97.8	100.0	AF534183.1:2970-4245	TetA is a tetracycline efflux pump found in many species of Gram-negative bacteria.	tetracycline
contig00001	277953	279440	tolC	0/0	100.0	99.7	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan
contig00004	49335	50978	yojI	0/0	100.0	98.7	U00096.3:2308615-2306971	YojI mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. YojI is capable of pumping out microcin molecules. The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI.	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00103	1585	2388	(AGly)strA	0/0	100.0	99.9	AB366441:22458-23261	(AGly)strA	NA
contig00103	749	1585	(AGly)strB	0/0	100.0	100.0	FJ474091:264-1100	(AGly)strB	NA
contig00013	50176	51480	(Bla)AmpC1_Ecoli	0/0	100.0	99.4	FN649414:2765051-2766355	(Bla)AmpC1_Ecoli	NA
contig00019	48520	49653	(Bla)AmpC2_Ecoli	0/0	100.0	97.3	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00003	47670	48827	(Bla)ampH_Ecoli	0/0	100.0	98.9	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00036	35508	36383	(Bla)blaCTX-M-55	0/0	100.0	100.0	HM748991:321-1196	(Bla)blaCTX-M-55	NA
contig00075	1306	2445	(Bla)blaDHA-1	0/0	100.0	100.0	HM193083:987-2126	(Bla)blaDHA-1	NA
contig00064	9630	10490	(Bla)blaTEM-105	0/0	100.0	99.9	AF516720:215-1075	(Bla)blaTEM-105	NA
contig00002	150013	151914	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100.0	99.7	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA
contig00064	3612	4268	(Flq)qnr-S1	0/0	100.0	100.0	AB187515:9737-10393	(Flq)qnr-S1	NA
contig00075	6566	7213	(Flq)qnrB4	0/0	100.0	100.0	DQ303921:4-648	(Flq)qnrB4	NA
contig00117	288	1025	(MLS)erm(B)	0/0	100.0	99.6	M11180:714-1451	(MLS)erm(B)	NA
contig00162	1	882	(MLS)mph(A)	0/0	97.3	100.0	DQ445270:1626-2531	(MLS)mph(A)	NA
contig00082	250	1089	(Sul)sul1	0/0	100.0	100.0	AF071413:6700-7539	(Sul)sul1	NA
contig00103	2449	3264	(Sul)sul2	0/0	100.0	100.0	EU360945:1617-2432	(Sul)sul2	NA
contig00064	11798	13072	(Tet)tetA	0/0	100.0	100.0	JX424423:94438-95712	(Tet)tetA	NA
contig00177	182	655	(Tmt)dfrA14	0/0	100.0	100.0	GU726917:72-545	(Tmt)dfrA14	NA
contig00158	460	933	(Tmt)dfrA17	0/0	100.0	100.0	AB126604:98-571	(Tmt)dfrA17	NA
contig00125	300	773	(Tmt)dhfr7	0/0	100.0	100.0	X58425:594-1067	(Tmt)dhfr7	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00103	1585	2412	aph(3’’)-Ib	0/0	100.0	100.0	NG_056002.2	aminoglycoside O-phosphotransferase APH(3’’)-Ib	STREPTOMYCIN
contig00103	749	1585	aph(6)-Id	0/0	100.0	100.0	NG_047464.1	aminoglycoside O-phosphotransferase APH(6)-Id	STREPTOMYCIN
contig00036	35508	36383	blaCTX-M-55	0/0	100.0	100.0	NG_049006.1	class A extended-spectrum beta-lactamase CTX-M-55	CEPHALOSPORIN
contig00075	1306	2445	blaDHA-1	0/0	100.0	100.0	NG_049055.1	class C beta-lactamase DHA-1	CEPHALOSPORIN
contig00019	48520	49653	blaEC-15	0/0	100.0	98.6	NG_049081.1	class C extended-spectrum beta-lactamase EC-15	CEPHALOSPORIN
contig00064	9630	10490	blaTEM-1	0/0	100.0	100.0	NG_050145.1	class A broad-spectrum beta-lactamase TEM-1	BETA-LACTAM
contig00177	182	655	dfrA14	0/0	100.0	100.0	NG_056035.1	trimethoprim-resistant dihydrofolate reductase DfrA14	TRIMETHOPRIM
contig00158	460	933	dfrA17	0/0	100.0	99.8	NG_047710.1	trimethoprim-resistant dihydrofolate reductase DfrA17	TRIMETHOPRIM
contig00125	300	773	dfrA7	0/0	100.0	100.0	NG_047737.1	trimethoprim-resistant dihydrofolate reductase DfrA7	TRIMETHOPRIM
contig00117	288	1025	erm(B)	0/0	100.0	99.9	NG_047804.1	23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(B)	MACROLIDE
contig00162	1	882	mph(A)	0/0	97.3	100.0	NG_047985.1	Mph(A) family macrolide 2’-phosphotransferase	MACROLIDE
contig00075	6569	7213	qnrB4	0/0	100.0	100.0	NG_050502.1	quinolone resistance pentapeptide repeat protein QnrB4	QUINOLONE
contig00064	3612	4268	qnrS1	0/0	100.0	100.0	NG_050543.1	quinolone resistance pentapeptide repeat protein QnrS1	QUINOLONE
contig00082	250	1089	sul1	0/0	100.0	100.0	NG_048082.1	sulfonamide-resistant dihydropteroate synthase Sul1	SULFONAMIDE
contig00103	2449	3264	sul2	0/0	100.0	100.0	NG_051852.1	sulfonamide-resistant dihydropteroate synthase Sul2	SULFONAMIDE
contig00064	11798	12997	tet(A)	0/0	100.0	100.0	NG_048154.1	tetracycline efflux MFS transporter Tet(A)	TETRACYCLINE

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00003	136965	138158	ACRA	0/0	100.0	99.8	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00003	133793	136942	ACRB	0/0	100.0	99.5	MEG_401	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRB	NA
contig00013	15665	18778	ACRD	0/0	100.0	98.9	MEG_407	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ACRD	NA
contig00044	8641	9798	ACRE	0/0	100.0	98.9	MEG_408	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRE	NA
contig00044	5525	8629	ACRF	0/0	100.0	99.0	MEG_409	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRF	NA
contig00044	10197	10859	ACRS	0/0	100.0	99.1	MEG_415	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS	NA
contig00003	47670	48827	AMPH	0/0	100.0	98.9	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00103	1585	2412	APH3-DPRIME	0/0	100.0	100.0	MEG_1019	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH3-DPRIME	NA
contig00103	749	1585	APH6	0/0	100.0	100.0	MEG_1086	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH6	NA
contig00027	32054	33906	ASMA	0/0	100.0	96.8	MEG_1180	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:ASMA	NA
contig00001	301816	302637	BACA	0/0	100.0	100.0	MEG_1190	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00027	9118	9840	BAER	0/0	100.0	97.8	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00027	9837	11240	BAES	0/0	100.0	99.3	MEG_1193	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES	NA
contig00004	22872	24062	BCR	0/0	100.0	96.7	MEG_1210	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR	NA
contig00019	48520	49653	BLAEC	0/0	100.0	98.6	MEG_1282	Drugs:betalactams:Class_C_betalactamases:BLAEC	NA
contig00026	22147	22845	CPXAR	0/0	100.0	99.9	MEG_2118	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00026	22842	24215	CPXAR	0/0	100.0	98.5	MEG_2121	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00010	14930	15562	CRP	0/0	100.0	99.4	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00036	35262	36754	CTX	1/7	100.0	99.3	MEG_2421	Drugs:betalactams:Class_A_betalactamases:CTX	NA
contig00125	300	773	DFRA	0/0	100.0	100.0	MEG_2548	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00158	460	933	DFRA	0/0	100.0	100.0	MEG_2547	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00177	182	655	DFRA	0/0	100.0	99.8	MEG_2517	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00075	1306	2445	DHA	0/0	100.0	100.0	MEG_2585	Drugs:betalactams:Class_C_betalactamases:DHA	NA
contig00016	26008	27180	EMRA	0/0	100.0	98.1	MEG_2722	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA	NA
contig00016	27197	28735	EMRB	0/0	100.0	99.3	MEG_2725	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRB	NA
contig00006	92158	93348	EMRD	0/0	100.0	99.8	MEG_2729	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD	NA
contig00058	16778	17941	EMRK	0/0	100.0	99.9	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig00016	25351	25881	EMRR	0/0	100.0	100.0	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00058	15240	16778	EMRY	0/0	100.0	99.0	MEG_2736	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRY	NA
contig00052	1560	3203	EPTA	0/0	100.0	99.8	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig00117	262	1025	ERMB	2/2	100.0	99.0	MEG_2801	Drugs:MLS:23S_rRNA_methyltransferases:ERMB	NA
contig00013	110122	113715	EVGS	0/0	100.0	100.0	MEG_2870	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EVGS	NA
contig00045	2243	2971	GADW	0/0	100.0	98.6	MEG_3081	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig00045	1051	1875	GADX	0/0	100.0	97.7	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00017	22891	23304	HNS	0/0	100.0	99.5	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00002	95589	96266	KDPE	0/0	100.0	99.3	MEG_3448	Drugs:Aminoglycosides:Aminoglycoside_efflux_pumps:KDPE	NA
contig00039	13393	13782	MARA	0/0	100.0	99.2	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00039	12945	13379	MARR	0/0	100.0	97.5	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00011	56271	57503	MDFA	0/0	100.0	100.0	MEG_3737	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDFA	NA
contig00027	18853	20100	MDTA	0/0	100.0	97.2	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00027	15731	18853	MDTB	0/0	100.0	96.9	MEG_3747	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTB	NA
contig00027	12653	15730	MDTC	0/0	100.0	97.6	MEG_3749	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTC	NA
contig00045	6472	7629	MDTE	0/0	100.0	99.7	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00045	3334	6447	MDTF	0/0	100.0	98.5	MEG_3752	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTF	NA
contig00022	72668	73894	MDTG	0/0	100.0	100.0	MEG_3753	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig00022	62829	64037	MDTH	0/0	100.0	97.9	MEG_3755	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTH	NA
contig00034	21537	21866	MDTI	0/0	100.0	100.0	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00034	21853	22218	MDTJ	0/0	100.0	99.5	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00007	113635	115008	MDTK	0/0	100.0	99.0	MEG_3759	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:MDTK	NA
contig00020	77	1108	MDTN	0/0	100.0	100.0	MEG_3763	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN	NA
contig00020	1108	3159	MDTO	0/0	100.0	99.1	MEG_3764	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTO	NA
contig00020	3156	4622	MDTP	0/0	100.0	99.9	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig00162	1	882	MPHA	0/0	97.3	100.0	MEG_4029	Drugs:MLS:Macrolide_phosphotransferases:MPHA	NA
contig00012	5046	5522	MPHB	0/0	100.0	98.1	MEG_4033	Drugs:MLS:Macrolide_phosphotransferases:MPHB	NA
contig00009	71622	73370	MSBA	0/0	100.0	100.0	MEG_4061	Drugs:Multi-drug_resistance:Multi-drug_ABC_efflux_pumps:MSBA	NA
contig00104	2538	2870	MVRC	0/0	100.0	91.9	MEG_4103	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MVRC	NA
contig00002	150013	151914	PBP2	0/0	100.0	99.7	MEG_5400	Drugs:betalactams:Penicillin_binding_protein:PBP2	NA
contig00013	50176	51480	PBP4B	0/0	100.0	99.4	MEG_5409	Drugs:betalactams:Penicillin_binding_protein:PBP4B	NA
contig00004	102028	102996	PMRF	0/0	100.0	99.6	MEG_5801	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF	NA
contig00075	6566	7213	QNRB	0/0	100.0	100.0	MEG_5932	Drugs:Fluoroquinolones:Quinolone_resistance_protein_Qnr:QNRB	NA
contig00064	3612	4268	QNRS	0/0	100.0	100.0	MEG_6020	Drugs:Fluoroquinolones:Quinolone_resistance_protein_Qnr:QNRS	NA
contig00023	57085	57954	ROBA	0/0	100.0	99.1	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00020	26691	27013	SOXS	0/0	99.7	99.7	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00082	249	1216	SULI	0/0	100.0	100.0	MEG_6615	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULI	NA
contig00103	2449	3264	SULII	0/0	100.0	100.0	MEG_6617	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULII	NA
contig00064	9263	10508	TEM	0/0	98.3	99.4	MEG_6875	Drugs:betalactams:Class_A_betalactamases:TEM	NA
contig00064	11798	13072	TETA	0/0	100.0	100.0	MEG_7024	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETA	NA
contig00004	49335	50978	YOGI	0/0	100.0	98.7	MEG_7842	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:YOGI	NA

ID086II

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00066	1696	2556	aac(3)-IIa_1	0/0	100.0	99.8	X51534	aac(3)-IIa	Gentamicin, Tobramycin
contig00050	1303	2091	aadA5_1	0/0	100.0	100.0	AF137361	aadA5	Streptomycin
contig00061	971	1774	aph(3’’)-Ib_5	0/0	100.0	100.0	AF321551	aph(3’’)-Ib	Streptomycin
contig00061	135	971	aph(6)-Id_1	0/0	100.0	99.9	M28829	aph(6)-Id	Streptomycin
contig00053	2407	3282	blaCTX-M-15_1	0/0	100.0	100.0	AY044436	blaCTX-M-15	Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig00050	699	1172	dfrA17_1	0/0	100.0	100.0	FJ460238	dfrA17	Trimethoprim
contig00001	29919	31151	mdf(A)_1	0/0	100.0	97.8	Y08743	mdf(A)
contig00077	69	990	mph(A)_2	1/1	100.0	99.7	U36578	mph(A)	Erythromycin, Azithromycin, Spiramycin, Telithromycin
contig00050	2611	3477	sul1_5	0/0	100.0	99.9	EU780013	sul1	Sulfamethoxazole
contig00061	1835	2650	sul2_2	0/0	100.0	100.0	AY034138	sul2	Sulfamethoxazole
contig00062	1435	2681	tet(A)_6	0/0	97.8	100.0	AF534183	tet(A)	Doxycycline, Tetracycline

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00066	1696	2556	AAC(3)-IIe	0/0	100.0	99.5	EU022315.1:0-861	AAC(3)-IIe is a plasmid-encoded aminoglycoside acetyltransferase in E. coli	aminoglycoside
contig00050	1303	2091	aadA5	0/0	100.0	100.0	AF137361:63-852	aadA5 is an aminoglycoside nucleotidyltransferase gene encoded by plasmids transposons and integrons in E. coli K. pneumoniae Kluyvera georgiana P. aeruginosa and E. cloacae	aminoglycoside
contig00001	410564	413713	acrB	0/0	100.0	98.8	U00096.3:484403-481253	Protein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug/proton antiporter.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00006	99480	102593	acrD	0/0	100.0	98.7	AP009048.1:2586250-2589364	AcrD is an aminoglycoside efflux pump expressed in E. coli. Its expression can be induced by indole and is regulated by baeRS and cpxAR.	aminoglycoside
contig00011	149301	150458	acrE	0/0	100.0	98.8	U00096:3413863-3415021	AcrE is a membrane fusion protein similar to AcrA.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00011	150470	153574	acrF	0/0	100.0	96.6	U00096:3415032-3418137	AcrF is a inner membrane transporter similar to AcrB.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00011	148240	148902	acrS	0/0	100.0	98.3	U00096:3413465-3412802	AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.	cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00061	971	1774	APH(3’’)-Ib	0/0	100.0	99.8	AF313472:15593-16397	APH(3’’)-Ib is an aminoglycoside phosphotransferase encoded by plasmids transposons integrative conjugative elements and chromosomes in Enterobacteriaceae and Pseudomonas spp.	aminoglycoside
contig00061	135	971	APH(6)-Id	0/0	100.0	99.8	AF024602:3155-3992	APH(6)-Id is an aminoglycoside phosphotransferase encoded by plasmids integrative conjugative elements and chromosomal genomic islands in K. pneumoniae Salmonella spp. E. coli Shigella flexneri Providencia alcalifaciens Pseudomonas spp. V. cholerae Edwardsiella tarda Pasteurella multocida and Aeromonas bestiarum	aminoglycoside
contig00007	52237	53056	bacA	0/0	99.8	98.3	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00002	336794	337515	baeR	0/0	99.9	97.1	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00002	337512	338915	baeS	0/0	100.0	90.5	AP009048:2165012-2166416	BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.	aminocoumarin, aminoglycoside
contig00016	66576	67943	cpxA	0/0	99.6	98.5	BA000007.3:4905062-4903688	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	aminocoumarin, aminoglycoside
contig00012	15089	15721	CRP	0/0	100.0	99.2	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00053	2407	3282	CTX-M-15	0/0	100.0	100.0	AY044436:1435-2311	CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family	cephalosporin
contig00050	699	1172	dfrA17	0/0	100.0	100.0	DQ838665:0-474	dfrA17 is an integron-encoded dihydrofolate reductase found in Escherichia coli	diaminopyrimidine
contig00025	60096	61268	emrA	0/0	100.0	98.0	AP009048:2810082-2811255	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	fluoroquinolone
contig00025	61285	62823	emrB	0/0	100.0	98.4	U00096:2812615-2814154	emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin.	fluoroquinolone
contig00006	5710	6765	emrK	0/0	100.0	97.7	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00025	59439	59969	emrR	0/0	100.0	98.5	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00006	4172	5710	emrY	0/0	100.0	97.7	D78168:1591-3130	emrY is a multidrug transport that moves substrates across the inner membrane of the Gram-negative E. coli. It is a homolog of emrB.	tetracycline
contig00008	146399	148042	eptA	0/0	100.0	91.4	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00001	409348	410541	Escherichia_coli_acrA	0/0	100.0	99.1	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00022	48073	49206	Escherichia_coli_ampC	0/0	100.0	97.8	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00001	498463	499620	Escherichia_coli_ampH	0/0	100.0	97.1	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig00013	28735	29067	Escherichia_coli_emrE	0/0	100.0	92.2	Z11877.1:485-818	Member of the small MDR (multidrug resistance) family of transporters, in Escherichia coli this protein provides resistance against a number of positively charged compounds including ethidium bromide and erythromycin, proton-dependent secondary transporter which exchanges protons for compound translocation	macrolide
contig00001	29919	31151	Escherichia_coli_mdfA	0/0	100.0	96.3	JQ394987:0-1233	Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter.	benzalkonium_chloride, rhodamine, tetracycline
contig00006	7289	7903	evgA	0/0	100.0	99.0	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00006	7908	11501	evgS	0/0	100.0	96.3	U00096:2484373-2487967	EvgS is a sensor protein that phosphorylates the regulatory protein EvgA. evgS corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	fluoroquinolone, macrolide, penam, tetracycline
contig00029	1556	2284	gadW	0/0	100.0	100.0	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig00029	363	1187	gadX	0/0	100.0	93.9	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00020	39527	39940	H-NS	0/0	100.0	99.3	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00001	185272	185944	kdpE	0/0	99.3	95.5	U00096.3:721733-721055	kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding.	aminoglycoside
contig00004	289457	289840	marA	0/0	100.0	99.0	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00002	346528	347775	mdtA	0/0	100.0	95.6	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00002	343406	346528	mdtB	0/0	100.0	96.2	U00096:2155262-2158385	MdtB is a transporter that forms a heteromultimer complex with MdtC to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex.	aminocoumarin
contig00002	340328	343405	mdtC	0/0	100.0	94.0	U00096:2158385-2161463	MdtC is a transporter that forms a heteromultimer complex with MdtB to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex. In the absence of MdtB MdtC can form a homomultimer complex that results in a functioning efflux complex with a narrower drug specificity. mdtC corresponds to 3 loci in Pseudomonas aeruginosa PAO1 (gene name: muxC/muxB) and 3 loci in Pseudomonas aeruginosa LESB58.	aminocoumarin
contig00029	5785	6942	mdtE	0/0	100.0	98.5	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00029	2647	5760	mdtF	0/0	100.0	97.3	U00096:3660413-3663527	MdtF is the multidrug inner membrane transporter for the MdtEF-TolC efflux complex.	fluoroquinolone, macrolide, penam
contig00010	91831	93057	mdtG	0/0	100.0	98.4	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00010	81994	83202	mdtH	0/0	100.0	98.3	U00096:1125326-1124117	Multidrug resistance protein MdtH	fluoroquinolone
contig00003	306754	307986	mdtM	0/0	100.0	95.0	U00096.3:4568519-4567286	Multidrug resistance protein MdtM	acridine_dye, fluoroquinolone, lincosamide, nucleoside, phenicol
contig00008	116126	117157	mdtN	0/0	100.0	96.2	AP009048.1:4307588-4306556	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	acridine_dye, nucleoside
contig00008	114075	116126	mdtO	0/0	100.0	97.0	AP009048.1:4306557-4304505	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00008	112612	114078	mdtP	0/0	100.0	97.6	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00077	69	974	mphA	0/0	100.0	100.0	D16251.1:2531-1625	The mphA gene encodes for resistance enzyme MPH(2’)-I which preferentially inactivate 14-membered macrolides (e.g.erythromycin telithromycin roxithromycin) over 16-membered macrolides (e.g.tylosin spiramycin). It phosphorylates macrolides at 2’-OH hydroxyl of desosamine sugar of macrolides in a GTP-dependent manner.	macrolide
contig00015	45415	47163	msbA	0/0	100.0	98.1	U00096.3:966620-968369	MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability.	nitroimidazole
contig00002	102789	103757	pmrF	0/0	100.0	97.6	U00096:2367070-2368039	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide
contig00050	2638	3477	sul1	0/0	100.0	100.0	JF969163:1053-1893	Sul1 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria. It is linked to other resistance genes of class 1 integrons.	sulfonamide
contig00061	1835	2650	sul2	0/0	100.0	100.0	AY055428.1:21084-20268	Sul2 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria usually found on small plasmids.	sulfonamide
contig00062	1435	2681	tet(A)	0/0	97.8	100.0	AF534183.1:2970-4245	TetA is a tetracycline efflux pump found in many species of Gram-negative bacteria.	tetracycline
contig00007	78739	80226	tolC	0/0	100.0	98.2	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan
contig00002	400871	402037	ugd	0/0	100.0	96.0	U00096:2099613-2098446	PmrE is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin	peptide
contig00002	161962	163605	yojI	0/0	100.0	97.4	U00096.3:2308615-2306971	YojI mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. YojI is capable of pumping out microcin molecules. The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI.	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00066	1696	2556	(AGly)aac3-IIa	0/0	100	99.8	X51534:91-951	(AGly)aac3-IIa	NA
contig00050	1303	2091	(AGly)aadA5	0/0	100	100.0	AF137361:64-852	(AGly)aadA5	NA
contig00061	971	1774	(AGly)strA	0/0	100	99.9	AB366441:22458-23261	(AGly)strA	NA
contig00061	135	971	(AGly)strB	0/0	100	99.9	FJ474091:264-1100	(AGly)strB	NA
contig00022	48073	49206	(Bla)AmpC2_Ecoli	0/0	100	97.8	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00001	498463	499620	(Bla)ampH_Ecoli	0/0	100	97.1	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00053	2407	3282	(Bla)blaCTX-M-15	0/0	100	100.0	JQ686199:261-1136	(Bla)blaCTX-M-15	NA
contig00001	244490	246391	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100	98.7	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA
contig00077	69	974	(MLS)mph(A)	0/0	100	100.0	DQ445270:1626-2531	(MLS)mph(A)	NA
contig00050	2638	3477	(Sul)sul1	0/0	100	100.0	AF071413:6700-7539	(Sul)sul1	NA
contig00061	1835	2650	(Sul)sul2	0/0	100	100.0	EU360945:1617-2432	(Sul)sul2	NA
contig00062	1407	2681	(Tet)tetA	0/0	100	100.0	JX424423:94438-95712	(Tet)tetA	NA
contig00050	699	1172	(Tmt)dfrA17	0/0	100	100.0	AB126604:98-571	(Tmt)dfrA17	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00066	1696	2556	aac(3)-IIe	0/0	100	99.8	NG_047244.1	aminoglycoside N-acetyltransferase AAC(3)-IIe	GENTAMICIN
contig00050	1303	2091	aadA5	0/0	100	100.0	NG_047357.1	ANT(3’’)-Ia family aminoglycoside nucleotidyltransferase AadA5	STREPTOMYCIN
contig00061	971	1798	aph(3’’)-Ib	0/0	100	100.0	NG_056002.2	aminoglycoside O-phosphotransferase APH(3’’)-Ib	STREPTOMYCIN
contig00061	135	971	aph(6)-Id	0/0	100	100.0	NG_047466.1	aminoglycoside O-phosphotransferase APH(6)-Id	STREPTOMYCIN
contig00053	2407	3282	blaCTX-M-15	0/0	100	100.0	NG_048935.1	class A extended-spectrum beta-lactamase CTX-M-15	CEPHALOSPORIN
contig00022	48073	49206	blaEC-5	0/0	100	99.5	NG_049085.1	cephalosporin-hydrolyzing class C beta-lactamase EC-5	CEPHALOSPORIN
contig00050	699	1172	dfrA17	0/0	100	99.8	NG_047710.1	trimethoprim-resistant dihydrofolate reductase DfrA17	TRIMETHOPRIM
contig00077	69	990	mph(A)	1/1	100	99.7	NG_047986.1	Mph(A) family macrolide 2’-phosphotransferase	MACROLIDE
contig00050	2638	3477	sul1	0/0	100	100.0	NG_048082.1	sulfonamide-resistant dihydropteroate synthase Sul1	SULFONAMIDE
contig00061	1835	2650	sul2	0/0	100	100.0	NG_051852.1	sulfonamide-resistant dihydropteroate synthase Sul2	SULFONAMIDE
contig00062	1407	2606	tet(A)	0/0	100	100.0	NG_048154.1	tetracycline efflux MFS transporter Tet(A)	TETRACYCLINE

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00066	1696	2556	AAC3	0/0	100.0	99.8	MEG_44	Drugs:Aminoglycosides:Aminoglycoside_N-acetyltransferases:AAC3	NA
contig00001	409348	410541	ACRA	0/0	100.0	99.1	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00001	410564	413713	ACRB	0/0	100.0	98.8	MEG_401	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRB	NA
contig00006	99480	102593	ACRD	0/0	100.0	98.7	MEG_407	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ACRD	NA
contig00011	149301	150458	ACRE	0/0	100.0	98.8	MEG_408	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRE	NA
contig00011	150470	153574	ACRF	0/0	100.0	96.6	MEG_409	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRF	NA
contig00011	148240	148902	ACRS	0/0	100.0	98.3	MEG_415	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS	NA
contig00001	498463	499620	AMPH	0/0	100.0	97.1	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00050	1303	2091	ANT3-DPRIME	0/0	100.0	100.0	MEG_928	Drugs:Aminoglycosides:Aminoglycoside_O-nucleotidyltransferases:ANT3-DPRIME	NA
contig00061	971	1798	APH3-DPRIME	0/0	100.0	100.0	MEG_1019	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH3-DPRIME	NA
contig00061	135	971	APH6	0/0	100.0	100.0	MEG_1084	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH6	NA
contig00002	359435	361287	ASMA	0/0	100.0	97.6	MEG_1180	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:ASMA	NA
contig00007	52237	53056	BACA	0/0	99.8	98.5	MEG_1189	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00002	336794	337515	BAER	0/0	99.9	97.1	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00002	337512	338915	BAES	0/0	100.0	90.5	MEG_1193	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES	NA
contig00002	187238	188428	BCR	0/0	100.0	96.6	MEG_1210	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR	NA
contig00022	48073	49206	BLAEC	0/0	100.0	99.5	MEG_1275	Drugs:betalactams:Class_C_betalactamases:BLAEC	NA
contig00016	65881	66579	CPXAR	0/0	100.0	98.0	MEG_2118	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00016	66576	67943	CPXAR	0/0	99.6	99.0	MEG_2121	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00012	15089	15721	CRP	0/0	100.0	99.2	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00050	699	1172	DFRA	0/0	100.0	100.0	MEG_2547	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00025	60096	61268	EMRA	0/0	100.0	98.0	MEG_2722	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA	NA
contig00025	61285	62823	EMRB	0/0	100.0	98.4	MEG_2725	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRB	NA
contig00005	194231	195421	EMRD	0/0	100.0	97.5	MEG_2729	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD	NA
contig00006	5710	6873	EMRK	0/0	100.0	97.4	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig00025	59439	59969	EMRR	0/0	100.0	98.5	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00006	4172	5710	EMRY	0/0	100.0	97.7	MEG_2736	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRY	NA
contig00008	146399	148042	EPTA	0/0	100.0	91.4	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig00006	7908	11501	EVGS	0/0	100.0	97.4	MEG_2869	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EVGS	NA
contig00029	1556	2284	GADW	0/0	100.0	100.0	MEG_3082	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig00029	363	1187	GADX	0/0	100.0	93.9	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00020	39527	39940	HNS	0/0	100.0	99.3	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00001	185272	185944	KDPE	0/0	99.3	95.5	MEG_3448	Drugs:Aminoglycosides:Aminoglycoside_efflux_pumps:KDPE	NA
contig00004	289457	289846	MARA	0/0	100.0	99.0	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00004	289861	290295	MARR	0/0	100.0	98.2	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00001	29919	31151	MDFA	0/0	100.0	97.9	MEG_3737	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDFA	NA
contig00002	346528	347775	MDTA	0/0	100.0	95.6	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00002	343406	346528	MDTB	0/0	100.0	96.2	MEG_3747	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTB	NA
contig00002	340328	343405	MDTC	0/0	100.0	94.0	MEG_3749	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTC	NA
contig00029	5785	6942	MDTE	0/0	100.0	98.5	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00029	2647	5760	MDTF	0/0	100.0	97.3	MEG_3752	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTF	NA
contig00010	91831	93057	MDTG	0/0	100.0	98.5	MEG_3753	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig00010	81994	83202	MDTH	0/0	100.0	98.3	MEG_3755	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTH	NA
contig00004	258563	258892	MDTI	0/0	100.0	98.8	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00004	258211	258576	MDTJ	0/0	100.0	98.4	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00004	191249	192621	MDTK	0/0	99.9	97.7	MEG_3759	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:MDTK	NA
contig00003	306754	307986	MDTM	0/0	100.0	95.0	MEG_3761	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTM	NA
contig00008	116126	117157	MDTN	0/0	100.0	96.2	MEG_3763	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN	NA
contig00008	114075	116126	MDTO	0/0	100.0	97.0	MEG_3764	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTO	NA
contig00008	112612	114078	MDTP	0/0	100.0	97.6	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig00077	69	990	MPHA	1/1	100.0	99.7	MEG_4030	Drugs:MLS:Macrolide_phosphotransferases:MPHA	NA
contig00015	45415	47163	MSBA	0/0	100.0	98.1	MEG_4061	Drugs:Multi-drug_resistance:Multi-drug_ABC_efflux_pumps:MSBA	NA
contig00013	28735	29067	MVRC	0/0	100.0	92.2	MEG_4103	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MVRC	NA
contig00001	244490	246391	PBP2	0/0	100.0	98.7	MEG_5400	Drugs:betalactams:Penicillin_binding_protein:PBP2	NA
contig00002	102789	103757	PMRF	0/0	100.0	97.6	MEG_5801	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF	NA
contig00003	247278	248147	ROBA	0/0	100.0	99.0	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00008	84259	84581	SOXS	0/0	99.7	98.1	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00050	2637	3604	SULI	0/0	100.0	100.0	MEG_6615	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULI	NA
contig00061	1835	2650	SULII	0/0	100.0	100.0	MEG_6617	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULII	NA
contig00062	1407	2681	TETA	0/0	100.0	100.0	MEG_7024	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETA	NA
contig00002	400871	402037	UGD	0/0	100.0	96.0	MEG_7328	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:UGD	NA
contig00002	161962	163605	YOGI	0/0	100.0	97.4	MEG_7842	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:YOGI	NA

ID088

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00080	1696	2556	aac(3)-IIa_1	0/0	100	99.8	X51534	aac(3)-IIa	Gentamicin, Tobramycin
contig00085	1539	2138	aac(6’)-Ib-cr_1	0/0	100	100.0	DQ303918	aac(6’)-Ib-cr	Ciprofloxacin
contig00070	1702	2490	aadA5_1	0/0	100	100.0	AF137361	aadA5	Streptomycin
contig00062	5421	6200	aph(3’’)-Ib_5	0/0	97	100.0	AF321551	aph(3’’)-Ib	Streptomycin
contig00062	4585	5421	aph(6)-Id_1	0/0	100	100.0	M28829	aph(6)-Id	Streptomycin
contig00068	1587	2462	blaCTX-M-15_1	0/0	100	100.0	AY044436	blaCTX-M-15	Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig00085	578	1408	blaOXA-1_1	0/0	100	100.0	HQ170510	blaOXA-1	Amoxicillin, Amoxicillin+Clavulanic_acid, Ampicillin, Ampicillin+Clavulanic_acid, Cefepime, Piperacillin, Piperacillin+Tazobactam
contig00070	2621	3094	dfrA17_1	0/0	100	100.0	FJ460238	dfrA17	Trimethoprim
contig00001	151006	152238	mdf(A)_1	0/0	100	99.9	Y08743	mdf(A)
contig00096	68	989	mph(A)_2	1/1	100	99.7	U36578	mph(A)	Erythromycin, Azithromycin, Spiramycin, Telithromycin
contig00070	316	1182	sul1_5	0/0	100	99.9	EU780013	sul1	Sulfamethoxazole
contig00062	85	900	sul2_2	0/0	100	100.0	AY034138	sul2	Sulfamethoxazole
contig00063	1998	3203	tet(B)_2	0/0	100	100.0	AF326777	tet(B)	Doxycycline, Tetracycline, Minocycline

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00080	1696	2556	AAC(3)-IIe	0/0	100.0	99.5	EU022315.1:0-861	AAC(3)-IIe is a plasmid-encoded aminoglycoside acetyltransferase in E. coli	aminoglycoside
contig00085	1539	2138	AAC(6’)-Ib-cr	0/0	100.0	100.0	DQ303918:0-600	AAC(6’)-Ib-cr is an aminoglycoside acetyltransferase encoded by plasmids transposons integrons in Enterobacteriaceae. The aac(6’)-Ib-cr variant gene can induce resistance against aminoglycoside and fluoroquinolone simultaneously	aminoglycoside, fluoroquinolone
contig00070	1702	2490	aadA5	0/0	100.0	100.0	AF137361:63-852	aadA5 is an aminoglycoside nucleotidyltransferase gene encoded by plasmids transposons and integrons in E. coli K. pneumoniae Kluyvera georgiana P. aeruginosa and E. cloacae	aminoglycoside
contig00002	38756	41905	acrB	0/0	100.0	100.0	U00096.3:484403-481253	Protein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug/proton antiporter.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00007	148083	151196	acrD	0/0	100.0	98.8	AP009048.1:2586250-2589364	AcrD is an aminoglycoside efflux pump expressed in E. coli. Its expression can be induced by indole and is regulated by baeRS and cpxAR.	aminoglycoside
contig00059	5854	8958	acrF	0/0	100.0	100.0	U00096:3415032-3418137	AcrF is a inner membrane transporter similar to AcrB.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00034	602	1264	acrS	0/0	100.0	100.0	U00096:3413465-3412802	AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.	cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00062	5421	6200	APH(3’’)-Ib	0/0	97.0	99.7	AF313472:15593-16397	APH(3’’)-Ib is an aminoglycoside phosphotransferase encoded by plasmids transposons integrative conjugative elements and chromosomes in Enterobacteriaceae and Pseudomonas spp.	aminoglycoside
contig00062	4585	5421	APH(6)-Id	0/0	100.0	99.9	AF024602:3155-3992	APH(6)-Id is an aminoglycoside phosphotransferase encoded by plasmids integrative conjugative elements and chromosomal genomic islands in K. pneumoniae Salmonella spp. E. coli Shigella flexneri Providencia alcalifaciens Pseudomonas spp. V. cholerae Edwardsiella tarda Pasteurella multocida and Aeromonas bestiarum	aminoglycoside
contig00004	70314	71133	bacA	0/0	99.8	98.5	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00027	57252	57974	baeR	0/0	100.0	99.0	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00027	55852	57255	baeS	0/0	100.0	98.7	AP009048:2165012-2166416	BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.	aminocoumarin, aminoglycoside
contig00018	25022	26395	cpxA	0/0	100.0	99.0	BA000007.3:4905062-4903688	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	aminocoumarin, aminoglycoside
contig00009	15377	16009	CRP	0/0	100.0	99.7	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00068	1587	2462	CTX-M-15	0/0	100.0	100.0	AY044436:1435-2311	CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family	cephalosporin
contig00070	2621	3094	dfrA17	0/0	100.0	100.0	DQ838665:0-474	dfrA17 is an integron-encoded dihydrofolate reductase found in Escherichia coli	diaminopyrimidine
contig00010	58703	59875	emrA	0/0	100.0	97.9	AP009048:2810082-2811255	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	fluoroquinolone
contig00010	59892	61430	emrB	0/0	100.0	98.6	U00096:2812615-2814154	emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin.	fluoroquinolone
contig00005	178467	179522	emrK	0/0	100.0	98.0	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00010	58046	58576	emrR	0/0	100.0	99.4	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00005	176929	178467	emrY	0/0	100.0	97.7	D78168:1591-3130	emrY is a multidrug transport that moves substrates across the inner membrane of the Gram-negative E. coli. It is a homolog of emrB.	tetracycline
contig00008	81599	83242	eptA	0/0	100.0	99.9	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00002	37540	38733	Escherichia_coli_acrA	0/0	100.0	100.0	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00008	38238	39371	Escherichia_coli_ampC	0/0	100.0	97.3	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00007	183082	184386	Escherichia_coli_ampC1_beta-lactamase	0/0	100.0	95.9	FN649414.1:2765050-2766355	An ampC-like beta-lactamase identified from Escherichia coli.	cephalosporin, penam
contig00002	126872	128029	Escherichia_coli_ampH	0/0	100.0	100.0	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig00001	151006	152238	Escherichia_coli_mdfA	0/0	100.0	98.4	JQ394987:0-1233	Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter.	benzalkonium_chloride, rhodamine, tetracycline
contig00005	180046	180660	evgA	0/0	100.0	99.2	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00005	180665	184258	evgS	0/0	100.0	96.8	U00096:2484373-2487967	EvgS is a sensor protein that phosphorylates the regulatory protein EvgA. evgS corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	fluoroquinolone, macrolide, penam, tetracycline
contig00037	1784	2512	gadW	0/0	100.0	94.7	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig00037	592	1416	gadX	0/0	100.0	100.0	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00033	5443	5856	H-NS	0/0	100.0	99.3	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00011	8563	9240	kdpE	0/0	100.0	100.0	U00096.3:721733-721055	kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding.	aminoglycoside
contig00023	30978	31361	marA	0/0	100.0	100.0	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00027	46992	48239	mdtA	0/0	100.0	98.1	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00027	48239	51361	mdtB	0/0	100.0	99.9	U00096:2155262-2158385	MdtB is a transporter that forms a heteromultimer complex with MdtC to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex.	aminocoumarin
contig00027	51362	54439	mdtC	0/0	100.0	97.7	U00096:2158385-2161463	MdtC is a transporter that forms a heteromultimer complex with MdtB to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex. In the absence of MdtB MdtC can form a homomultimer complex that results in a functioning efflux complex with a narrower drug specificity. mdtC corresponds to 3 loci in Pseudomonas aeruginosa PAO1 (gene name: muxC/muxB) and 3 loci in Pseudomonas aeruginosa LESB58.	aminocoumarin
contig00037	6013	7170	mdtE	0/0	100.0	100.0	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00037	2875	5988	mdtF	0/0	100.0	100.0	U00096:3660413-3663527	MdtF is the multidrug inner membrane transporter for the MdtEF-TolC efflux complex.	fluoroquinolone, macrolide, penam
contig00032	29396	30622	mdtG	0/0	100.0	99.4	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00032	19560	20768	mdtH	0/0	100.0	99.9	U00096:1125326-1124117	Multidrug resistance protein MdtH	fluoroquinolone
contig00019	70066	71298	mdtM	0/0	100.0	96.3	U00096.3:4568519-4567286	Multidrug resistance protein MdtM	acridine_dye, fluoroquinolone, lincosamide, nucleoside, phenicol
contig00008	112980	114011	mdtN	0/0	100.0	100.0	AP009048.1:4307588-4306556	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	acridine_dye, nucleoside
contig00008	114011	116062	mdtO	0/0	100.0	100.0	AP009048.1:4306557-4304505	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00008	116059	117525	mdtP	0/0	100.0	100.0	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00096	68	973	mphA	0/0	100.0	100.0	D16251.1:2531-1625	The mphA gene encodes for resistance enzyme MPH(2’)-I which preferentially inactivate 14-membered macrolides (e.g.erythromycin telithromycin roxithromycin) over 16-membered macrolides (e.g.tylosin spiramycin). It phosphorylates macrolides at 2’-OH hydroxyl of desosamine sugar of macrolides in a GTP-dependent manner.	macrolide
contig00007	126902	127376	mphB	0/0	99.6	96.2	AE005174.2:3397370-3397847	The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides.	macrolide
contig00001	233954	235702	msbA	0/0	100.0	100.0	U00096.3:966620-968369	MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability.	nitroimidazole
contig00085	578	1408	OXA-1	0/0	100.0	100.0	JN420336.1:2230-1399	OXA-1 is a beta-lactamase found in E. coli	cephalosporin, penam
contig00005	63954	64922	pmrF	0/0	100.0	98.0	U00096:2367070-2368039	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide
contig00070	316	1155	sul1	0/0	100.0	100.0	JF969163:1053-1893	Sul1 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria. It is linked to other resistance genes of class 1 integrons.	sulfonamide
contig00062	85	900	sul2	0/0	100.0	100.0	AY055428.1:21084-20268	Sul2 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria usually found on small plasmids.	sulfonamide
contig00063	1998	3203	tet(B)	0/0	100.0	99.8	AB089595:0-1206	Tet(B) is a tetracycline efflux protein expressed in many Gram-negative bacteria. It confers resistance to tetracycline doxycycline and minocycline but not tigecycline.	tetracycline
contig00004	46547	48034	tolC	0/0	100.0	99.9	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan
contig00005	2079	3722	yojI	0/0	100.0	100.0	U00096.3:2308615-2306971	YojI mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. YojI is capable of pumping out microcin molecules. The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI.	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00080	1696	2556	(AGly)aac3-IIa	0/0	100	99.8	X51534:91-951	(AGly)aac3-IIa	NA
contig00070	1702	2490	(AGly)aadA5	0/0	100	100.0	AF137361:64-852	(AGly)aadA5	NA
contig00062	5421	6200	(AGly)strA	0/0	97	99.9	AB366441:22458-23261	(AGly)strA	NA
contig00062	4585	5421	(AGly)strB	0/0	100	100.0	FJ474091:264-1100	(AGly)strB	NA
contig00007	183082	184386	(Bla)AmpC1_Ecoli	0/0	100	95.9	FN649414:2765051-2766355	(Bla)AmpC1_Ecoli	NA
contig00008	38238	39371	(Bla)AmpC2_Ecoli	0/0	100	97.3	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00002	126872	128029	(Bla)ampH_Ecoli	0/0	100	100.0	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00068	1587	2462	(Bla)blaCTX-M-15	0/0	100	100.0	JQ686199:261-1136	(Bla)blaCTX-M-15	NA
contig00085	578	1408	(Bla)blaOXA-1	0/0	100	100.0	JQ682867:1-831	(Bla)blaOXA-1	NA
contig00011	60650	62551	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100	100.0	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA
contig00096	68	973	(MLS)mph(A)	0/0	100	100.0	DQ445270:1626-2531	(MLS)mph(A)	NA
contig00070	316	1155	(Sul)sul1	0/0	100	100.0	AF071413:6700-7539	(Sul)sul1	NA
contig00062	85	900	(Sul)sul2	0/0	100	100.0	EU360945:1617-2432	(Sul)sul2	NA
contig00063	1998	3203	(Tet)tetB	0/0	100	99.7	AB089594:1-1206	(Tet)tetB	NA
contig00070	2621	3094	(Tmt)dfrA17	0/0	100	100.0	AB126604:98-571	(Tmt)dfrA17	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00080	1696	2556	aac(3)-IIe	0/0	100.0	99.8	NG_047244.1	aminoglycoside N-acetyltransferase AAC(3)-IIe	GENTAMICIN
contig00085	1539	2093	aac(6’)-Ib-D181Y	0/0	100.0	99.8	NG_067946.1	AAC(6’)-Ib family aminoglycoside 6’-N-acetyltransferase	AMIKACIN, KANAMYCIN, TOBRAMYCIN
contig00070	1702	2490	aadA5	0/0	100.0	100.0	NG_047357.1	ANT(3’’)-Ia family aminoglycoside nucleotidyltransferase AadA5	STREPTOMYCIN
contig00062	5421	6200	aph(3’’)-Ib	0/0	94.2	100.0	NG_056002.2	aminoglycoside O-phosphotransferase APH(3’’)-Ib	STREPTOMYCIN
contig00062	4585	5421	aph(6)-Id	0/0	100.0	100.0	NG_047464.1	aminoglycoside O-phosphotransferase APH(6)-Id	STREPTOMYCIN
contig00068	1587	2462	blaCTX-M-15	0/0	100.0	100.0	NG_048935.1	class A extended-spectrum beta-lactamase CTX-M-15	CEPHALOSPORIN
contig00008	38238	39371	blaEC-15	0/0	100.0	98.5	NG_049081.1	class C extended-spectrum beta-lactamase EC-15	CEPHALOSPORIN
contig00085	578	1408	blaOXA-1	0/0	100.0	100.0	NG_049392.1	oxacillin-hydrolyzing class D beta-lactamase OXA-1	CEPHALOSPORIN
contig00070	2621	3094	dfrA17	0/0	100.0	99.8	NG_047710.1	trimethoprim-resistant dihydrofolate reductase DfrA17	TRIMETHOPRIM
contig00096	68	989	mph(A)	1/1	100.0	99.7	NG_047986.1	Mph(A) family macrolide 2’-phosphotransferase	MACROLIDE
contig00070	316	1155	sul1	0/0	100.0	100.0	NG_048082.1	sulfonamide-resistant dihydropteroate synthase Sul1	SULFONAMIDE
contig00062	85	900	sul2	0/0	100.0	100.0	NG_051852.1	sulfonamide-resistant dihydropteroate synthase Sul2	SULFONAMIDE
contig00063	1998	3203	tet(B)	0/0	100.0	100.0	NG_048163.1	tetracycline efflux MFS transporter Tet(B)	TETRACYCLINE

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00080	1696	2556	AAC3	0/0	100.0	99.8	MEG_44	Drugs:Aminoglycosides:Aminoglycoside_N-acetyltransferases:AAC3	NA
contig00002	37540	38733	ACRA	0/0	100.0	100.0	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00002	38756	41905	ACRB	0/0	100.0	100.0	MEG_401	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRB	NA
contig00007	148083	151196	ACRD	0/0	100.0	98.8	MEG_407	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ACRD	NA
contig00059	5854	8958	ACRF	0/0	100.0	100.0	MEG_409	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRF	NA
contig00034	602	1264	ACRS	0/0	100.0	100.0	MEG_415	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS	NA
contig00002	126872	128029	AMPH	0/0	100.0	100.0	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00070	1702	2490	ANT3-DPRIME	0/0	100.0	100.0	MEG_928	Drugs:Aminoglycosides:Aminoglycoside_O-nucleotidyltransferases:ANT3-DPRIME	NA
contig00062	5421	6200	APH3-DPRIME	0/0	94.2	100.0	MEG_1019	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH3-DPRIME	NA
contig00062	4585	5421	APH6	0/0	100.0	100.0	MEG_1086	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH6	NA
contig00027	32874	34726	ASMA	0/0	100.0	97.2	MEG_1180	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:ASMA	NA
contig00004	70314	71133	BACA	0/0	99.8	98.8	MEG_1189	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00027	57252	57974	BAER	0/0	100.0	99.0	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00027	55852	57255	BAES	0/0	100.0	98.7	MEG_1193	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES	NA
contig00015	67338	68528	BCR	0/0	100.0	100.0	MEG_1210	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR	NA
contig00008	38238	39371	BLAEC	0/0	100.0	98.5	MEG_1282	Drugs:betalactams:Class_C_betalactamases:BLAEC	NA
contig00018	24327	25025	CPXAR	0/0	100.0	100.0	MEG_2122	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00018	25022	26395	CPXAR	0/0	100.0	100.0	MEG_2121	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00009	15377	16009	CRP	0/0	100.0	99.7	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00099	62	1004	CTX	0/0	100.0	98.2	MEG_2435	Drugs:betalactams:Class_A_betalactamases:CTX	NA
contig00070	2621	3094	DFRA	0/0	100.0	100.0	MEG_2547	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00010	58703	59875	EMRA	0/0	100.0	97.9	MEG_2722	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA	NA
contig00010	59892	61430	EMRB	0/0	100.0	98.6	MEG_2725	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRB	NA
contig00035	43174	44364	EMRD	0/0	100.0	100.0	MEG_2729	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD	NA
contig00005	178467	179630	EMRK	0/0	100.0	98.2	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig00010	58046	58576	EMRR	0/0	100.0	99.4	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00005	176929	178467	EMRY	0/0	100.0	97.7	MEG_2736	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRY	NA
contig00008	81599	83242	EPTA	0/0	100.0	99.9	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig00005	180665	184258	EVGS	0/0	100.0	97.2	MEG_2869	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EVGS	NA
contig00037	1784	2512	GADW	0/0	100.0	100.0	MEG_3081	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig00037	592	1416	GADX	0/0	100.0	100.0	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00033	5443	5856	HNS	0/0	100.0	99.3	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00011	8563	9240	KDPE	0/0	100.0	100.0	MEG_3448	Drugs:Aminoglycosides:Aminoglycoside_efflux_pumps:KDPE	NA
contig00023	30972	31361	MARA	0/0	100.0	100.0	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00023	30524	30958	MARR	0/0	100.0	100.0	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00001	151006	152238	MDFA	0/0	100.0	100.0	MEG_3737	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDFA	NA
contig00027	46992	48239	MDTA	0/0	100.0	98.1	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00027	48239	51361	MDTB	0/0	100.0	99.9	MEG_3747	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTB	NA
contig00027	51362	54439	MDTC	0/0	100.0	97.7	MEG_3749	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTC	NA
contig00037	6013	7170	MDTE	0/0	100.0	100.0	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00037	2875	5988	MDTF	0/0	100.0	100.0	MEG_3752	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTF	NA
contig00032	29396	30622	MDTG	0/0	100.0	100.0	MEG_3753	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig00032	19560	20768	MDTH	0/0	100.0	99.9	MEG_3755	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTH	NA
contig00023	63754	64083	MDTI	0/0	100.0	100.0	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00023	64070	64435	MDTJ	0/0	100.0	99.5	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00021	26477	27850	MDTK	0/0	100.0	100.0	MEG_3759	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:MDTK	NA
contig00019	70066	71298	MDTM	0/0	100.0	96.3	MEG_3761	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTM	NA
contig00008	112980	114011	MDTN	0/0	100.0	100.0	MEG_3763	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN	NA
contig00008	114011	116062	MDTO	0/0	100.0	100.0	MEG_3764	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTO	NA
contig00008	116059	117525	MDTP	0/0	100.0	100.0	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig00096	68	989	MPHA	1/1	100.0	99.7	MEG_4030	Drugs:MLS:Macrolide_phosphotransferases:MPHA	NA
contig00007	126902	127376	MPHB	0/0	99.6	96.2	MEG_4033	Drugs:MLS:Macrolide_phosphotransferases:MPHB	NA
contig00001	233954	235702	MSBA	0/0	100.0	100.0	MEG_4061	Drugs:Multi-drug_resistance:Multi-drug_ABC_efflux_pumps:MSBA	NA
contig00085	578	1408	OXA	0/0	100.0	100.0	MEG_4980	Drugs:betalactams:Class_D_betalactamases:OXA	NA
contig00011	60650	62551	PBP2	0/0	100.0	100.0	MEG_5400	Drugs:betalactams:Penicillin_binding_protein:PBP2	NA
contig00007	183082	184386	PBP4B	0/0	100.0	95.9	MEG_5409	Drugs:betalactams:Penicillin_binding_protein:PBP4B	NA
contig00005	63954	64922	PMRF	0/0	100.0	98.0	MEG_5801	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF	NA
contig00019	21724	22593	ROBA	0/0	100.0	99.0	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00008	139141	139464	SOXS	0/0	100.0	100.0	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00070	189	1156	SULI	0/0	100.0	100.0	MEG_6615	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULI	NA
contig00062	85	900	SULII	0/0	100.0	100.0	MEG_6617	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULII	NA
contig00063	1998	3203	TETB	0/0	100.0	100.0	MEG_7052	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETB	NA
contig00063	3997	4413	TETD	0/0	100.0	100.0	MEG_7070	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETD	NA
contig00005	2079	3722	YOGI	0/0	100.0	100.0	MEG_7842	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:YOGI	NA

ID092

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig01130	1694	2554	aac(3)-IIa_1	0/0	100.0	99.8	X51534	aac(3)-IIa	Gentamicin, Tobramycin
contig01320	1539	2138	aac(6’)-Ib-cr_1	0/0	100.0	100.0	DQ303918	aac(6’)-Ib-cr	Ciprofloxacin
contig00354	2651	3439	aadA5_1	0/0	100.0	100.0	AF137361	aadA5	Streptomycin
contig01566	941	1744	aph(3’’)-Ib_5	0/0	100.0	100.0	AF321551	aph(3’’)-Ib	Streptomycin
contig01566	105	941	aph(6)-Id_1	0/0	100.0	99.9	M28829	aph(6)-Id	Streptomycin
contig00031	20968	22119	blaADC-25_1	0/0	100.0	97.0	EF016355	blaADC-25
contig00439	2211	3086	blaCTX-M-15_1	0/0	100.0	100.0	AY044436	blaCTX-M-15	Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig02022	93	905	blaNDM-1_1	0/0	100.0	100.0	FN396876	blaNDM-1	Amoxicillin, Amoxicillin+Clavulanic_acid, Ampicillin, Ampicillin+Clavulanic_acid, Cefepime, Cefixime, Cefotaxime, Cefoxitin, Ceftazidime, Ertapenem, Imipenem, Meropenem, Piperacillin, Piperacillin+Tazobactam
contig01320	578	1408	blaOXA-1_1	0/0	100.0	100.0	HQ170510	blaOXA-1	Amoxicillin, Amoxicillin+Clavulanic_acid, Ampicillin, Ampicillin+Clavulanic_acid, Cefepime, Piperacillin, Piperacillin+Tazobactam
contig01535	180	1004	blaOXA-70_1	0/0	100.0	100.0	AY750912	blaOXA-70
contig00354	2047	2520	dfrA17_1	0/0	100.0	100.0	FJ460238	dfrA17	Trimethoprim
contig02107	42	551	dfrA8_1	0/0	100.0	100.0	U10186	dfrA8	Trimethoprim
contig01093	596	1828	mdf(A)_1	0/0	100.0	98.5	Y08743	mdf(A)
contig00252	6770	7691	mph(A)_2	1/1	100.0	99.6	U36578	mph(A)	Erythromycin, Azithromycin, Spiramycin, Telithromycin
contig00332	5131	5787	qnrS1_1	0/0	100.0	100.0	AB187515	qnrS1	Ciprofloxacin
contig00354	3959	4825	sul1_5	0/0	100.0	99.9	EU780013	sul1	Sulfamethoxazole
contig02150	327	1139	sul2_2	0/0	99.6	100.0	AY034138	sul2	Sulfamethoxazole
contig01230	1069	2274	tet(B)_1	0/0	100.0	100.0	AP000342	tet(B)	Doxycycline, Tetracycline, Minocycline

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig01130	1694	2554	AAC(3)-IIe	0/0	100.0	99.5	EU022315.1:0-861	AAC(3)-IIe is a plasmid-encoded aminoglycoside acetyltransferase in E. coli	aminoglycoside
contig01320	1539	2138	AAC(6’)-Ib-cr	0/0	100.0	100.0	DQ303918:0-600	AAC(6’)-Ib-cr is an aminoglycoside acetyltransferase encoded by plasmids transposons integrons in Enterobacteriaceae. The aac(6’)-Ib-cr variant gene can induce resistance against aminoglycoside and fluoroquinolone simultaneously	aminoglycoside, fluoroquinolone
contig00354	2651	3439	aadA5	0/0	100.0	100.0	AF137361:63-852	aadA5 is an aminoglycoside nucleotidyltransferase gene encoded by plasmids transposons and integrons in E. coli K. pneumoniae Kluyvera georgiana P. aeruginosa and E. cloacae	aminoglycoside
contig00006	19310	20656	abeM	0/0	100.0	98.9	AB204810:186-1533	AbeM is an multidrug efflux pump found in Acinetobacter baumannii.	acridine_dye, fluoroquinolone, triclosan
contig00004	483	812	abeS	0/0	100.0	98.5	CP001172.1:1249348-1249018	AbeS in an efflux pump of the SMR family of transporters found in Acinetobacter baumannii.	aminocoumarin, macrolide
contig00789	2432	3671	Acinetobacter_baumannii_AbaF	0/0	96.1	98.5	CP000521.1:1558523-1557233	Expression of abaF in E. coli resulted in increased resistance to fosfomycin.	fosfomycin
contig00031	20968	22119	Acinetobacter_baumannii_AmpC_beta-lactamase	0/0	100.0	98.3	CP001182.1:2873299-2874451	A class C beta-lactamase found in Acinetobacter baumannii that confers resistance to piperacillin and cefepime.	cephalosporin, penam
contig00212	7818	9296	Acinetobacter_baumannii_AmvA	0/0	100.0	97.1	FJ911554.1:176-1655	AmvA has 14 alpha-helical transmembrane segments qualifying it as a member of the DHA2 transporter family of the major facilitator superfamily (MFS). When AmvA was expressed in E. coli the cells had at least four-fold decreased susceptibility to erythromycin acridine orange acriflavine deoxycholate and methyl viologen. AmvA from the AC0037 strain of A. baumannii was tested.	acridine_dye, macrolide
contig00678	384	3488	acrF	0/0	100.0	98.7	U00096:3415032-3418137	AcrF is a inner membrane transporter similar to AcrB.	cephalosporin, cephamycin, fluoroquinolone, penam
contig02064	607	1207	acrS	1/1	90.7	99.2	U00096:3413465-3412802	AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.	cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig02965	104	705	acrS	0/0	90.8	97.8	U00096:3413465-3412802	AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.	cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00956	1082	2299	adeG	1/3	99.8	96.9	CT025800.2:0-1221	AdeG is the inner membrane transporter of the AdeFGH multidrug efflux complex.	fluoroquinolone, tetracycline
contig00806	37	1488	adeH	0/0	100.0	98.3	CT025802.2:0-1452	AdeH is the outer membrane channel protein of the AdeFGH multidrug efflux complex.	fluoroquinolone, tetracycline
contig00017	19701	20951	adeI	0/0	100.0	99.8	CP001182.2:3283426-3284677	AdeI is the membrane fusion protein of the AdeIJK multidrug efflux complex.	carbapenem, cephalosporin, diaminopyrimidine, fluoroquinolone, lincosamide, macrolide, penem, phenicol, rifamycin, tetracycline
contig00017	20964	24140	adeJ	0/0	100.0	99.7	AY769962:2434-5611	AdeJ is a RND efflux protein that acts as the inner membrane transporter of the AdeIJK efflux complex. It has 57% identity with E. coli AcrB.	carbapenem, cephalosporin, diaminopyrimidine, fluoroquinolone, lincosamide, macrolide, penem, phenicol, rifamycin, tetracycline
contig00017	24140	25594	adeK	0/0	100.0	98.8	AY769962:5610-7065	AdeK is the outer membrane factor protein in the adeIJK multidrug efflux complex.	carbapenem, cephalosporin, diaminopyrimidine, fluoroquinolone, lincosamide, macrolide, penem, phenicol, rifamycin, tetracycline
contig00952	1191	1844	adeN	0/0	100.0	98.6	KF147862:0-654	AdeN is a repressor of AdeIJK a RND-type efflux pump in Acinetobacter baumannii. Its inactivation increases expression of AdeJ.	carbapenem, cephalosporin, diaminopyrimidine, fluoroquinolone, lincosamide, macrolide, penem, phenicol, rifamycin, tetracycline
contig01566	941	1744	APH(3’’)-Ib	0/0	100.0	99.8	AF313472:15593-16397	APH(3’’)-Ib is an aminoglycoside phosphotransferase encoded by plasmids transposons integrative conjugative elements and chromosomes in Enterobacteriaceae and Pseudomonas spp.	aminoglycoside
contig01566	105	941	APH(6)-Id	0/0	100.0	99.8	AF024602:3155-3992	APH(6)-Id is an aminoglycoside phosphotransferase encoded by plasmids integrative conjugative elements and chromosomal genomic islands in K. pneumoniae Salmonella spp. E. coli Shigella flexneri Providencia alcalifaciens Pseudomonas spp. V. cholerae Edwardsiella tarda Pasteurella multocida and Aeromonas bestiarum	aminoglycoside
contig00055	17677	18496	bacA	0/0	99.8	98.7	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig01357	1167	1986	bacA	0/0	99.8	97.0	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00314	1	693	baeR	0/0	95.8	100.0	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00957	1	1398	baeS	0/0	99.6	100.0	AP009048:2165012-2166416	BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.	aminocoumarin, aminoglycoside
contig01504	891	1523	CRP	0/0	100.0	99.2	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00439	2211	3086	CTX-M-15	0/0	100.0	100.0	AY044436:1435-2311	CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family	cephalosporin
contig02022	909	1243	determinant_of_bleomycin_resistance	0/0	91.5	100.0	KC503911.1:9883-10249	A novel bleomycin resistance protein encoded by a metallo-beta-lactamase-associated ble gene. Expression of BRP(MBL) confers resistance to bleomycin and bleomycin-like antibiotics in Enterobacteriaceae and Acinetobacter where it is co-expressed with an MBL and controlled by the same promoter region.	glycopeptide
contig00354	2047	2520	dfrA17	0/0	100.0	100.0	DQ838665:0-474	dfrA17 is an integron-encoded dihydrofolate reductase found in Escherichia coli	diaminopyrimidine
contig02107	42	551	dfrA8	0/0	100.0	100.0	KJ174469:710-1220	dfrA8 is a transposon-encoded dihydrofolate reductase found in Salmonella enterica	diaminopyrimidine
contig00604	3241	4413	emrA	0/0	100.0	98.1	AP009048:2810082-2811255	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	fluoroquinolone
contig00604	1686	3224	emrB	0/0	100.0	98.6	U00096:2812615-2814154	emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin.	fluoroquinolone
contig00779	2371	3564	Escherichia_coli_acrA	0/0	100.0	99.7	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00898	305	1438	Escherichia_coli_ampC	0/0	100.0	97.7	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00299	1845	3149	Escherichia_coli_ampC1_beta-lactamase	0/0	100.0	96.7	FN649414.1:2765050-2766355	An ampC-like beta-lactamase identified from Escherichia coli.	cephalosporin, penam
contig01499	690	1847	Escherichia_coli_ampH	0/0	100.0	98.7	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig00032	9088	9420	Escherichia_coli_emrE	0/0	100.0	98.8	Z11877.1:485-818	Member of the small MDR (multidrug resistance) family of transporters, in Escherichia coli this protein provides resistance against a number of positively charged compounds including ethidium bromide and erythromycin, proton-dependent secondary transporter which exchanges protons for compound translocation	macrolide
contig01283	330	662	Escherichia_coli_emrE	0/0	100.0	91.9	Z11877.1:485-818	Member of the small MDR (multidrug resistance) family of transporters, in Escherichia coli this protein provides resistance against a number of positively charged compounds including ethidium bromide and erythromycin, proton-dependent secondary transporter which exchanges protons for compound translocation	macrolide
contig01093	596	1828	Escherichia_coli_mdfA	0/0	100.0	96.9	JQ394987:0-1233	Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter.	benzalkonium_chloride, rhodamine, tetracycline
contig00751	1258	1872	evgA	0/0	100.0	99.0	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig02978	1	579	evgA	0/0	94.2	99.3	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig01240	527	1351	gadX	0/0	100.0	97.9	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig01475	90	914	gadX	0/0	100.0	93.9	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00403	154	567	H-NS	0/0	100.0	99.5	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00204	4680	5352	kdpE	0/0	99.3	97.2	U00096.3:721733-721055	kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding.	aminoglycoside
contig00233	7551	7934	marA	0/0	100.0	99.5	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00287	5512	6759	mdtA	0/0	100.0	99.4	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig01965	249	1301	mdtE	0/0	90.9	99.6	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00981	152	1360	mdtH	0/0	100.0	98.5	U00096:1125326-1124117	Multidrug resistance protein MdtH	fluoroquinolone
contig00145	2274	3506	mdtM	0/0	100.0	96.1	U00096.3:4568519-4567286	Multidrug resistance protein MdtM	acridine_dye, fluoroquinolone, lincosamide, nucleoside, phenicol
contig01950	1	1154	mdtM	0/0	93.6	99.9	U00096.3:4568519-4567286	Multidrug resistance protein MdtM	acridine_dye, fluoroquinolone, lincosamide, nucleoside, phenicol
contig00338	2306	3337	mdtN	0/0	100.0	98.0	AP009048.1:4307588-4306556	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	acridine_dye, nucleoside
contig00338	3337	5388	mdtO	0/0	100.0	98.2	AP009048.1:4306557-4304505	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00338	5385	6851	mdtP	0/0	100.0	98.2	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00252	6786	7691	mphA	0/0	100.0	99.9	D16251.1:2531-1625	The mphA gene encodes for resistance enzyme MPH(2’)-I which preferentially inactivate 14-membered macrolides (e.g.erythromycin telithromycin roxithromycin) over 16-membered macrolides (e.g.tylosin spiramycin). It phosphorylates macrolides at 2’-OH hydroxyl of desosamine sugar of macrolides in a GTP-dependent manner.	macrolide
contig00629	2760	3236	mphB	0/0	100.0	98.1	AE005174.2:3397370-3397847	The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides.	macrolide
contig02022	93	905	NDM-1	0/0	100.0	100.0	FN396876:3219-2406	NDM-1 is a metallo-beta-lactamase isolated from Klebsiella pneumoniae with nearly complete resistance to all beta-lactam antibiotics.	carbapenem, cephalosporin, cephamycin, penam
contig01320	578	1408	OXA-1	0/0	100.0	100.0	JN420336.1:2230-1399	OXA-1 is a beta-lactamase found in E. coli	cephalosporin, penam
contig01535	180	1004	OXA-70	0/0	100.0	100.0	AY750912:0-825	OXA-70 is a beta-lactamase found in A. baumannii	cephalosporin, penam
contig01429	167	1135	pmrF	0/0	100.0	99.4	U00096:2367070-2368039	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide
contig00332	5131	5787	QnrS1	0/0	100.0	100.0	DQ485529.1:0-657	QnrS1 is a plasmid-mediated quinolone resistance protein found in Shigella flexneri	fluoroquinolone
contig00354	3986	4825	sul1	0/0	100.0	100.0	JF969163:1053-1893	Sul1 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria. It is linked to other resistance genes of class 1 integrons.	sulfonamide
contig02150	327	1139	sul2	0/0	99.6	100.0	AY055428.1:21084-20268	Sul2 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria usually found on small plasmids.	sulfonamide
contig01230	1069	2274	tet(B)	0/0	100.0	99.8	AB089595:0-1206	Tet(B) is a tetracycline efflux protein expressed in many Gram-negative bacteria. It confers resistance to tetracycline doxycycline and minocycline but not tigecycline.	tetracycline
contig01779	1	1435	tolC	0/0	96.4	98.4	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan
contig00516	3268	4911	yojI	0/0	100.0	98.0	U00096.3:2308615-2306971	YojI mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. YojI is capable of pumping out microcin molecules. The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI.	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig01130	1694	2554	(AGly)aac3-IIa	0/0	100.0	99.8	X51534:91-951	(AGly)aac3-IIa	NA
contig00354	2651	3439	(AGly)aadA5	0/0	100.0	100.0	AF137361:64-852	(AGly)aadA5	NA
contig00022	23822	24609	(AGly)ant(3’’)-IIa	0/0	99.9	99.1	NG_054648:101-889	(AGly)ant(3’’)-IIa	NA
contig01566	941	1744	(AGly)strA	0/0	100.0	99.9	AB366441:22458-23261	(AGly)strA	NA
contig01566	105	941	(AGly)strB	0/0	100.0	99.9	FJ474091:264-1100	(AGly)strB	NA
contig00299	1845	3149	(Bla)AmpC1_Ecoli	0/0	100.0	96.7	FN649414:2765051-2766355	(Bla)AmpC1_Ecoli	NA
contig00898	305	1438	(Bla)AmpC2_Ecoli	0/0	100.0	97.7	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig01499	690	1847	(Bla)ampH_Ecoli	0/0	100.0	98.7	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00031	20959	22119	(Bla)beta-lactamase_class-C	0/0	97.5	98.3	NC_010410:1184557-1185747	(Bla)beta-lactamase_class-C	NA
contig00439	2211	3086	(Bla)blaCTX-M-15	0/0	100.0	100.0	JQ686199:261-1136	(Bla)blaCTX-M-15	NA
contig02022	93	905	(Bla)blaNDM-1	0/0	100.0	100.0	JQ080305:1-813	(Bla)blaNDM-1	NA
contig01320	578	1408	(Bla)blaOXA-1	0/0	100.0	100.0	JQ682867:1-831	(Bla)blaOXA-1	NA
contig01535	180	1004	(Bla)blaOXA-70	0/0	100.0	100.0	AY750912:1-825	(Bla)blaOXA-70	NA
contig01807	1	668	(Bla)Mbl	0/0	96.0	99.8	NC_010410:c1997136-1996441	(Bla)Mbl	NA
contig00334	1	1809	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	95.1	99.3	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA
contig00021	9628	10590	(Bla)Zn-dependent_hydrolase	0/0	100.0	98.8	NC_010410:882015-882977	(Bla)Zn-dependent_hydrolase	NA
contig00332	5131	5787	(Flq)qnr-S1	0/0	100.0	100.0	AB187515:9737-10393	(Flq)qnr-S1	NA
contig00252	6786	7691	(MLS)mph(A)	0/0	100.0	99.9	DQ445270:1626-2531	(MLS)mph(A)	NA
contig00354	3986	4825	(Sul)sul1	0/0	100.0	100.0	AF071413:6700-7539	(Sul)sul1	NA
contig02150	327	1139	(Sul)sul2	0/0	99.6	100.0	EU360945:1617-2432	(Sul)sul2	NA
contig01230	1069	2274	(Tet)tetB	0/0	100.0	99.8	AB089594:1-1206	(Tet)tetB	NA
contig00354	2047	2520	(Tmt)dfrA17	0/0	100.0	100.0	AB126604:98-571	(Tmt)dfrA17	NA
contig02107	42	551	(Tmt)dfrA8	0/0	100.0	100.0	U10186:711-1220	(Tmt)dfrA8	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig01130	1694	2554	aac(3)-IIe	0/0	100.0	99.8	NG_047244.1	aminoglycoside N-acetyltransferase AAC(3)-IIe	GENTAMICIN
contig01320	1539	2093	aac(6’)-Ib-D181Y	0/0	100.0	99.8	NG_067946.1	AAC(6’)-Ib family aminoglycoside 6’-N-acetyltransferase	AMIKACIN, KANAMYCIN, TOBRAMYCIN
contig00354	2651	3439	aadA5	0/0	100.0	100.0	NG_047357.1	ANT(3’’)-Ia family aminoglycoside nucleotidyltransferase AadA5	STREPTOMYCIN
contig00022	23822	24609	ant(3’’)-IIa	0/0	99.9	99.1	NG_054648.1	aminoglycoside nucleotidyltransferase ANT(3’’)-IIa	SPECTINOMYCIN, STREPTOMYCIN
contig01566	941	1768	aph(3’’)-Ib	0/0	100.0	100.0	NG_056002.2	aminoglycoside O-phosphotransferase APH(3’’)-Ib	STREPTOMYCIN
contig01566	105	941	aph(6)-Id	0/0	100.0	100.0	NG_047466.1	aminoglycoside O-phosphotransferase APH(6)-Id	STREPTOMYCIN
contig00031	20968	22119	blaADC-203	0/0	100.0	100.0	NG_066483.1	class C beta-lactamase ADC-203	CEPHALOSPORIN
contig00439	2211	3086	blaCTX-M-15	0/0	100.0	100.0	NG_048935.1	class A extended-spectrum beta-lactamase CTX-M-15	CEPHALOSPORIN
contig00898	305	1438	blaEC-18	0/0	100.0	99.2	NG_049083.1	class C extended-spectrum beta-lactamase EC-18	CEPHALOSPORIN
contig02022	93	905	blaNDM-1	0/0	100.0	100.0	NG_049326.1	subclass B1 metallo-beta-lactamase NDM-1	CARBAPENEM
contig01320	578	1408	blaOXA-1	0/0	100.0	100.0	NG_049392.1	oxacillin-hydrolyzing class D beta-lactamase OXA-1	CEPHALOSPORIN
contig01535	180	1004	blaOXA-70	0/0	100.0	100.0	NG_049811.1	OXA-51 family carbapenem-hydrolyzing class D beta-lactamase OXA-70	CARBAPENEM
contig02022	909	1243	ble-MBL	0/0	91.5	100.0	NG_047559.1	bleomycin binding protein Ble-MBL	BLEOMYCIN
contig00354	2047	2520	dfrA17	0/0	100.0	99.8	NG_047710.1	trimethoprim-resistant dihydrofolate reductase DfrA17	TRIMETHOPRIM
contig02107	42	551	dfrA8	0/0	100.0	100.0	NG_047741.1	trimethoprim-resistant dihydrofolate reductase DfrA8	TRIMETHOPRIM
contig00252	6770	7691	mph(A)	1/1	100.0	99.6	NG_047986.1	Mph(A) family macrolide 2’-phosphotransferase	MACROLIDE
contig00332	5131	5787	qnrS1	0/0	100.0	100.0	NG_050543.1	quinolone resistance pentapeptide repeat protein QnrS1	QUINOLONE
contig00354	3986	4825	sul1	0/0	100.0	100.0	NG_048082.1	sulfonamide-resistant dihydropteroate synthase Sul1	SULFONAMIDE
contig02150	327	1139	sul2	0/0	99.6	100.0	NG_051852.1	sulfonamide-resistant dihydropteroate synthase Sul2	SULFONAMIDE
contig01230	1069	2274	tet(B)	0/0	100.0	100.0	NG_048161.1	tetracycline efflux MFS transporter Tet(B)	TETRACYCLINE

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig01130	1694	2554	AAC3	0/0	100.0	99.8	MEG_44	Drugs:Aminoglycosides:Aminoglycoside_N-acetyltransferases:AAC3	NA
contig00789	2432	3671	ABAF	0/0	96.1	98.5	MEG_369	Drugs:Fosfomycin:Fosfomycin_MFS_efflux_pump:ABAF	NA
contig00006	19310	20656	ABEM	0/0	100.0	98.9	MEG_372	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:ABEM	NA
contig00004	483	812	ABES	0/0	100.0	100.0	MEG_377	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:ABES	NA
contig00779	2371	3564	ACRA	0/0	100.0	99.7	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00678	384	3488	ACRF	0/0	100.0	98.7	MEG_409	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRF	NA
contig02064	607	1207	ACRS	1/1	90.7	99.2	MEG_415	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS	NA
contig02965	104	705	ACRS	0/0	90.8	97.8	MEG_415	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS	NA
contig00031	20959	22119	ADC	0/0	97.5	98.3	MEG_629	Drugs:betalactams:Class_C_betalactamases:ADC	NA
contig00806	37	1488	ADEH	0/0	100.0	98.3	MEG_685	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ADEH	NA
contig00017	19701	20951	ADEI	0/0	100.0	100.0	MEG_688	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ADEI	NA
contig00017	20964	24140	ADEJ	0/0	100.0	99.7	MEG_692	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ADEJ	NA
contig00017	24140	25594	ADEK	0/0	100.0	100.0	MEG_695	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ADEK	NA
contig00952	1191	1844	ADEN	0/0	100.0	99.1	MEG_701	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ADEN	NA
contig00046	15816	16532	ADET2	0/0	100.0	99.0	MEG_706	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ADET2	NA
contig01499	690	1847	AMPH	0/0	100.0	98.7	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00212	7818	9296	AMVA	0/0	100.0	97.1	MEG_733	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:AMVA	NA
contig00022	23822	24609	ANT3-DPRIME	0/0	99.9	99.1	MEG_899	Drugs:Aminoglycosides:Aminoglycoside_O-nucleotidyltransferases:ANT3-DPRIME	NA
contig00354	2651	3439	ANT3-DPRIME	0/0	100.0	100.0	MEG_928	Drugs:Aminoglycosides:Aminoglycoside_O-nucleotidyltransferases:ANT3-DPRIME	NA
contig01566	941	1768	APH3-DPRIME	0/0	100.0	100.0	MEG_1019	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH3-DPRIME	NA
contig01566	105	941	APH6	0/0	100.0	100.0	MEG_1084	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH6	NA
contig00197	3062	4914	ASMA	0/0	100.0	98.5	MEG_1180	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:ASMA	NA
contig00055	17677	18496	BACA	0/0	99.8	98.9	MEG_1189	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig01357	1167	1986	BACA	0/0	99.8	97.2	MEG_1189	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00314	1	693	BAER	0/0	95.8	100.0	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00957	1	1398	BAES	0/0	99.6	100.0	MEG_1193	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES	NA
contig00367	4020	5210	BCR	0/0	100.0	96.8	MEG_1210	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR	NA
contig00898	305	1438	BLAEC	0/0	100.0	99.2	MEG_1279	Drugs:betalactams:Class_C_betalactamases:BLAEC	NA
contig02022	909	1243	BRP	0/0	91.5	100.0	MEG_1477	Drugs:Glycopeptides:Bleomycin_resistance_protein:BRP	NA
contig01504	891	1523	CRP	0/0	100.0	99.2	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00354	2047	2520	DFRA	0/0	100.0	100.0	MEG_2547	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig02107	42	551	DFRA	0/0	100.0	100.0	MEG_2553	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00604	3241	4413	EMRA	0/0	100.0	98.1	MEG_2722	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA	NA
contig00604	1686	3224	EMRB	0/0	100.0	98.6	MEG_2725	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRB	NA
contig01671	461	1633	EMRD	0/0	98.5	99.7	MEG_2729	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD	NA
contig01708	446	1578	EMRD	0/0	95.1	97.8	MEG_2729	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD	NA
contig01240	527	1351	GADX	0/0	100.0	97.9	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig01475	90	914	GADX	0/0	100.0	93.9	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00403	154	567	HNS	0/0	100.0	99.5	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00204	4680	5352	KDPE	0/0	99.3	97.2	MEG_3448	Drugs:Aminoglycosides:Aminoglycoside_efflux_pumps:KDPE	NA
contig00233	7551	7940	MARA	0/0	100.0	99.5	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00233	7954	8388	MARR	0/0	100.0	98.2	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig01093	596	1828	MDFA	0/0	100.0	98.5	MEG_3737	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDFA	NA
contig00287	5512	6759	MDTA	0/0	100.0	99.4	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig01965	249	1301	MDTE	0/0	90.9	99.6	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00981	152	1360	MDTH	0/0	100.0	98.5	MEG_3755	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTH	NA
contig01989	690	1019	MDTI	0/0	100.0	99.4	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00450	3136	4509	MDTK	0/0	100.0	99.0	MEG_3759	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:MDTK	NA
contig00145	2274	3506	MDTM	0/0	100.0	96.1	MEG_3761	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTM	NA
contig01950	1	1154	MDTM	0/0	93.6	99.9	MEG_3761	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTM	NA
contig00338	2306	3337	MDTN	0/0	100.0	98.0	MEG_3763	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN	NA
contig00338	3337	5388	MDTO	0/0	100.0	98.2	MEG_3764	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTO	NA
contig00338	5385	6851	MDTP	0/0	100.0	98.2	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig00956	1082	2299	MEXE	0/0	100.0	99.0	MEG_3910	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MEXE	NA
contig00457	4761	5750	MEXT	0/0	100.0	99.2	MEG_3934	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MEXT	NA
contig00252	6770	7691	MPHA	1/1	100.0	99.6	MEG_4030	Drugs:MLS:Macrolide_phosphotransferases:MPHA	NA
contig00629	2760	3236	MPHB	0/0	100.0	98.1	MEG_4033	Drugs:MLS:Macrolide_phosphotransferases:MPHB	NA
contig00032	9088	9420	MVRC	0/0	100.0	98.8	MEG_4103	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MVRC	NA
contig01283	330	662	MVRC	0/0	100.0	91.9	MEG_4103	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MVRC	NA
contig02022	93	905	NDM	0/0	100.0	100.0	MEG_4143	Drugs:betalactams:Class_B_betalactamases:NDM	NA
contig01320	578	1408	OXA	0/0	100.0	100.0	MEG_4980	Drugs:betalactams:Class_D_betalactamases:OXA	NA
contig01535	98	1049	OXA	3/3	98.9	97.9	MEG_5236	Drugs:betalactams:Class_D_betalactamases:OXA	NA
contig00334	1	1809	PBP2	0/0	95.1	99.3	MEG_5400	Drugs:betalactams:Penicillin_binding_protein:PBP2	NA
contig00299	1845	3149	PBP4B	0/0	100.0	96.7	MEG_5409	Drugs:betalactams:Penicillin_binding_protein:PBP4B	NA
contig01429	167	1135	PMRF	0/0	100.0	99.4	MEG_5801	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF	NA
contig00332	5131	5787	QNRS	0/0	100.0	100.0	MEG_6020	Drugs:Fluoroquinolones:Quinolone_resistance_protein_Qnr:QNRS	NA
contig01709	91	960	ROBA	0/0	100.0	99.1	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig01715	163	485	SOXS	0/0	99.7	99.7	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00354	3985	4952	SULI	0/0	100.0	100.0	MEG_6615	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULI	NA
contig02150	327	1139	SULII	0/0	99.6	100.0	MEG_6617	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULII	NA
contig01230	1069	2274	TETB	0/0	100.0	100.0	MEG_7042	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETB	NA
contig00516	3268	4911	YOGI	0/0	100.0	98.0	MEG_7842	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:YOGI	NA

ID094LLFII

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00566	843	1646	aph(3’’)-Ib_5	0/0	100.0	100.0	AF321551	aph(3’’)-Ib	Streptomycin
contig00566	7	843	aph(6)-Id_1	0/0	100.0	100.0	M28829	aph(6)-Id	Streptomycin
contig00264	2861	3736	blaCTX-M-15_1	0/0	100.0	100.0	AY044436	blaCTX-M-15	Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig01160	619	1250	catA1_1	0/0	95.8	99.8	V00622	catA1	Chloramphenicol
contig00205	564	1046	dfrA14_5	0/0	100.0	99.6	DQ388123	dfrA14	Trimethoprim
contig00113	4302	5534	mdf(A)_1	0/0	100.0	98.1	Y08743	mdf(A)
contig00331	3505	4161	qnrS1_1	0/0	100.0	100.0	AB187515	qnrS1	Ciprofloxacin
contig00566	1707	2522	sul2_3	0/0	100.0	100.0	HQ840942	sul2	Sulfamethoxazole
contig00231	1997	3202	tet(B)_2	0/0	100.0	100.0	AF326777	tet(B)	Doxycycline, Tetracycline, Minocycline

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00294	2128	4947	acrD	0/0	90.6	98.8	AP009048.1:2586250-2589364	AcrD is an aminoglycoside efflux pump expressed in E. coli. Its expression can be induced by indole and is regulated by baeRS and cpxAR.	aminoglycoside
contig00618	1383	2045	acrS	0/0	100.0	98.9	U00096:3413465-3412802	AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.	cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00566	843	1646	APH(3’’)-Ib	0/0	100.0	99.8	AF313472:15593-16397	APH(3’’)-Ib is an aminoglycoside phosphotransferase encoded by plasmids transposons integrative conjugative elements and chromosomes in Enterobacteriaceae and Pseudomonas spp.	aminoglycoside
contig00566	7	843	APH(6)-Id	0/0	100.0	99.9	AF024602:3155-3992	APH(6)-Id is an aminoglycoside phosphotransferase encoded by plasmids integrative conjugative elements and chromosomal genomic islands in K. pneumoniae Salmonella spp. E. coli Shigella flexneri Providencia alcalifaciens Pseudomonas spp. V. cholerae Edwardsiella tarda Pasteurella multocida and Aeromonas bestiarum	aminoglycoside
contig00486	665	1484	bacA	0/0	99.8	96.2	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00050	6968	7689	baeR	0/0	99.9	97.9	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00050	5568	6971	baeS	0/0	100.0	96.4	AP009048:2165012-2166416	BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.	aminocoumarin, aminoglycoside
contig01160	619	1250	catI	0/0	95.8	99.8	V00622:243-903	catI is a chromosome and transposon-encoded variant of the cat gene found in Escherichia coli and Acinetobacter baumannii	phenicol
contig00500	680	1312	CRP	0/0	100.0	99.0	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00264	2861	3736	CTX-M-15	0/0	100.0	100.0	AY044436:1435-2311	CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family	cephalosporin
contig00205	564	1046	dfrA14	0/0	100.0	99.8	EU780012:2162-2645	dfrA14 is an integron-encoded dihydrofolate reductase found in Escherichia coli	diaminopyrimidine
contig01128	205	1289	emrA	0/0	92.5	97.9	AP009048:2810082-2811255	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	fluoroquinolone
contig00395	2417	3955	emrB	0/0	100.0	97.9	U00096:2812615-2814154	emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin.	fluoroquinolone
contig00154	3665	4720	emrK	0/0	100.0	97.8	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00154	2127	3665	emrY	0/0	100.0	97.5	D78168:1591-3130	emrY is a multidrug transport that moves substrates across the inner membrane of the Gram-negative E. coli. It is a homolog of emrB.	tetracycline
contig00593	1	1515	eptA	0/0	92.2	98.0	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00359	1	1071	Escherichia_coli_ampC	0/0	94.4	97.7	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00599	1175	2479	Escherichia_coli_ampC1_beta-lactamase	0/0	100.0	96.0	FN649414.1:2765050-2766355	An ampC-like beta-lactamase identified from Escherichia coli.	cephalosporin, penam
contig00093	4385	5542	Escherichia_coli_ampH	0/0	100.0	96.9	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig00113	4302	5534	Escherichia_coli_mdfA	0/0	100.0	96.6	JQ394987:0-1233	Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter.	benzalkonium_chloride, rhodamine, tetracycline
contig00154	5244	5858	evgA	0/0	100.0	99.0	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00734	512	1336	gadX	0/0	100.0	94.3	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00801	154	567	H-NS	0/0	100.0	99.5	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00032	7263	7940	kdpE	0/0	100.0	95.4	U00096.3:721733-721055	kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding.	aminoglycoside
contig00440	441	1688	mdtA	0/0	100.0	97.4	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00050	1078	4155	mdtC	0/0	100.0	97.1	U00096:2158385-2161463	MdtC is a transporter that forms a heteromultimer complex with MdtB to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex. In the absence of MdtB MdtC can form a homomultimer complex that results in a functioning efflux complex with a narrower drug specificity. mdtC corresponds to 3 loci in Pseudomonas aeruginosa PAO1 (gene name: muxC/muxB) and 3 loci in Pseudomonas aeruginosa LESB58.	aminocoumarin
contig01076	1	1119	mdtE	0/0	96.6	99.9	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig01034	286	1416	mdtG	0/0	92.2	98.6	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00965	414	1534	mdtH	0/0	92.7	97.9	U00096:1125326-1124117	Multidrug resistance protein MdtH	fluoroquinolone
contig00152	2989	4020	mdtN	0/0	100.0	96.4	AP009048.1:4307588-4306556	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	acridine_dye, nucleoside
contig00152	4020	6071	mdtO	0/0	100.0	96.3	AP009048.1:4306557-4304505	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00152	6068	7510	mdtP	0/0	98.4	97.5	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00174	2759	3233	mphB	0/0	99.6	96.6	AE005174.2:3397370-3397847	The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides.	macrolide
contig00153	3202	4950	msbA	0/0	100.0	99.0	U00096.3:966620-968369	MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability.	nitroimidazole
contig00159	4685	5653	pmrF	0/0	100.0	98.1	U00096:2367070-2368039	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide
contig00331	3505	4161	QnrS1	0/0	100.0	100.0	DQ485529.1:0-657	QnrS1 is a plasmid-mediated quinolone resistance protein found in Shigella flexneri	fluoroquinolone
contig00566	1707	2522	sul2	0/0	100.0	99.6	AY055428.1:21084-20268	Sul2 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria usually found on small plasmids.	sulfonamide
contig00231	1997	3202	tet(B)	0/0	100.0	99.8	AB089595:0-1206	Tet(B) is a tetracycline efflux protein expressed in many Gram-negative bacteria. It confers resistance to tetracycline doxycycline and minocycline but not tigecycline.	tetracycline
contig00031	9824	10990	ugd	0/0	100.0	97.5	U00096:2099613-2098446	PmrE is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00566	843	1646	(AGly)strA	0/0	100.0	99.9	AB366441:22458-23261	(AGly)strA	NA
contig00566	7	843	(AGly)strB	0/0	100.0	100.0	FJ474091:264-1100	(AGly)strB	NA
contig00599	1175	2479	(Bla)AmpC1_Ecoli	0/0	100.0	96.0	FN649414:2765051-2766355	(Bla)AmpC1_Ecoli	NA
contig00359	1	1071	(Bla)AmpC2_Ecoli	0/0	94.4	97.7	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00093	4385	5542	(Bla)ampH_Ecoli	0/0	100.0	96.9	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00264	2861	3736	(Bla)blaCTX-M-15	0/0	100.0	100.0	JQ686199:261-1136	(Bla)blaCTX-M-15	NA
contig00331	3505	4161	(Flq)qnr-S1	0/0	100.0	100.0	AB187515:9737-10393	(Flq)qnr-S1	NA
contig01160	619	1250	(Phe)catA1	0/0	95.8	99.8	V00622:244-903	(Phe)catA1	NA
contig00566	1707	2522	(Sul)sul2	0/0	100.0	99.6	EU360945:1617-2432	(Sul)sul2	NA
contig00231	1997	3202	(Tet)tetB	0/0	100.0	99.7	AB089594:1-1206	(Tet)tetB	NA
contig00205	564	1037	(Tmt)dfrA14	0/0	100.0	100.0	GU726917:72-545	(Tmt)dfrA14	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00566	843	1670	aph(3’’)-Ib	0/0	100.0	100.0	NG_056002.2	aminoglycoside O-phosphotransferase APH(3’’)-Ib	STREPTOMYCIN
contig00566	7	843	aph(6)-Id	0/0	100.0	100.0	NG_047464.1	aminoglycoside O-phosphotransferase APH(6)-Id	STREPTOMYCIN
contig00264	2861	3736	blaCTX-M-15	0/0	100.0	100.0	NG_048935.1	class A extended-spectrum beta-lactamase CTX-M-15	CEPHALOSPORIN
contig00359	1	1071	blaEC-8	0/0	94.4	98.3	NG_049086.1	cephalosporin-hydrolyzing class C beta-lactamase EC-8	CEPHALOSPORIN
contig01160	619	1250	catA1	0/0	95.8	99.8	NG_047582.1	type A-1 chloramphenicol O-acetyltransferase	CHLORAMPHENICOL
contig00205	564	1037	dfrA14	0/0	100.0	100.0	NG_056035.1	trimethoprim-resistant dihydrofolate reductase DfrA14	TRIMETHOPRIM
contig00331	3505	4161	qnrS1	0/0	100.0	100.0	NG_050543.1	quinolone resistance pentapeptide repeat protein QnrS1	QUINOLONE
contig00566	1707	2522	sul2	0/0	100.0	99.9	NG_048118.1	sulfonamide-resistant dihydropteroate synthase Sul2	SULFONAMIDE
contig00231	1997	3202	tet(B)	0/0	100.0	100.0	NG_048163.1	tetracycline efflux MFS transporter Tet(B)	TETRACYCLINE

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00294	2128	4947	ACRD	0/0	90.6	98.8	MEG_407	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ACRD	NA
contig00618	1383	2045	ACRS	0/0	100.0	98.9	MEG_415	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS	NA
contig00093	4385	5542	AMPH	0/0	100.0	96.9	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00566	843	1670	APH3-DPRIME	0/0	100.0	100.0	MEG_1019	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH3-DPRIME	NA
contig00566	7	843	APH6	0/0	100.0	100.0	MEG_1086	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH6	NA
contig00486	665	1484	BACA	0/0	99.8	96.7	MEG_1189	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00050	6968	7689	BAER	0/0	99.9	97.9	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00050	5568	6971	BAES	0/0	100.0	96.4	MEG_1193	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES	NA
contig00768	1	1059	BCR	0/0	93.4	97.3	MEG_1209	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR	NA
contig00359	1	1071	BLAEC	0/0	94.4	98.3	MEG_1278	Drugs:betalactams:Class_C_betalactamases:BLAEC	NA
contig01160	619	1250	CATA	0/0	95.8	100.0	MEG_1584	Drugs:Phenicol:Chloramphenicol_acetyltransferases:CATA	NA
contig00479	2394	3092	CPXAR	0/0	100.0	99.4	MEG_2118	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00500	680	1312	CRP	0/0	100.0	99.0	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00205	564	1037	DFRA	0/0	100.0	99.8	MEG_2517	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig01128	205	1289	EMRA	0/0	92.5	97.9	MEG_2722	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA	NA
contig00395	2417	3955	EMRB	0/0	100.0	97.9	MEG_2725	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRB	NA
contig00068	6066	7256	EMRD	0/0	100.0	97.6	MEG_2729	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD	NA
contig00154	3665	4828	EMRK	0/0	100.0	98.0	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig00154	2127	3665	EMRY	0/0	100.0	97.5	MEG_2736	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRY	NA
contig00593	1	1515	EPTA	0/0	92.2	98.0	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig00734	512	1336	GADX	0/0	100.0	94.3	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00801	154	567	HNS	0/0	100.0	99.5	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00032	7263	7940	KDPE	0/0	100.0	95.4	MEG_3448	Drugs:Aminoglycosides:Aminoglycoside_efflux_pumps:KDPE	NA
contig00460	2854	3288	MARR	0/0	100.0	97.9	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00113	4302	5534	MDFA	0/0	100.0	98.2	MEG_3737	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDFA	NA
contig00440	441	1688	MDTA	0/0	100.0	97.4	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00050	1078	4155	MDTC	0/0	100.0	97.1	MEG_3749	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTC	NA
contig01076	1	1119	MDTE	0/0	96.6	99.9	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig01034	286	1416	MDTG	0/0	92.2	98.8	MEG_3753	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig00965	414	1534	MDTH	0/0	92.7	97.9	MEG_3755	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTH	NA
contig00096	5101	5430	MDTI	0/0	100.0	99.7	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00096	5417	5782	MDTJ	0/0	100.0	98.1	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00406	1706	3078	MDTK	0/0	99.9	98.2	MEG_3759	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:MDTK	NA
contig00152	2989	4020	MDTN	0/0	100.0	96.4	MEG_3763	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN	NA
contig00152	4020	6071	MDTO	0/0	100.0	96.3	MEG_3764	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTO	NA
contig00152	6068	7510	MDTP	0/0	98.4	97.5	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig00174	2759	3233	MPHB	0/0	99.6	96.6	MEG_4033	Drugs:MLS:Macrolide_phosphotransferases:MPHB	NA
contig00153	3202	4950	MSBA	0/0	100.0	99.0	MEG_4061	Drugs:Multi-drug_resistance:Multi-drug_ABC_efflux_pumps:MSBA	NA
contig00599	1175	2479	PBP4B	0/0	100.0	96.0	MEG_5409	Drugs:betalactams:Penicillin_binding_protein:PBP4B	NA
contig00159	4685	5653	PMRF	0/0	100.0	98.1	MEG_5801	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF	NA
contig00331	3505	4161	QNRS	0/0	100.0	100.0	MEG_6020	Drugs:Fluoroquinolones:Quinolone_resistance_protein_Qnr:QNRS	NA
contig00052	1369	1691	SOXS	0/0	99.7	97.5	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00566	1707	2522	SULII	0/0	100.0	100.0	MEG_6618	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULII	NA
contig00231	1997	3202	TETB	0/0	100.0	100.0	MEG_7052	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETB	NA
contig00231	3996	4412	TETD	0/0	100.0	100.0	MEG_7070	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETD	NA
contig00031	9824	10990	UGD	0/0	100.0	97.5	MEG_7328	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:UGD	NA

ID099

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00004	34072	34947	blaCTX-M-15_1	0/0	100	100.0	AY044436	blaCTX-M-15	Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig00025	30075	31307	mdf(A)_1	0/0	100	99.1	Y08743	mdf(A)
contig00004	39588	40244	qnrS1_1	0/0	100	100.0	AB187515	qnrS1	Ciprofloxacin

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00008	124682	127831	acrB	0/0	100.0	99.1	U00096.3:484403-481253	Protein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug/proton antiporter.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00005	117709	120822	acrD	0/0	100.0	98.8	AP009048.1:2586250-2589364	AcrD is an aminoglycoside efflux pump expressed in E. coli. Its expression can be induced by indole and is regulated by baeRS and cpxAR.	aminoglycoside
contig00003	270325	271482	acrE	0/0	100.0	99.0	U00096:3413863-3415021	AcrE is a membrane fusion protein similar to AcrA.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00003	271494	274598	acrF	0/0	100.0	99.0	U00096:3415032-3418137	AcrF is a inner membrane transporter similar to AcrB.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00003	269264	269926	acrS	0/0	100.0	98.6	U00096:3413465-3412802	AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.	cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00003	60021	60840	bacA	0/0	99.8	98.7	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00015	11123	11845	baeR	0/0	100.0	99.5	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00015	11842	13245	baeS	0/0	100.0	98.7	AP009048:2165012-2166416	BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.	aminocoumarin, aminoglycoside
contig00030	22569	23942	cpxA	0/0	100.0	98.5	BA000007.3:4905062-4903688	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	aminocoumarin, aminoglycoside
contig00006	15358	15990	CRP	0/0	100.0	99.2	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00004	34072	34947	CTX-M-15	0/0	100.0	100.0	AY044436:1435-2311	CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family	cephalosporin
contig00002	27204	28376	emrA	0/0	100.0	98.2	AP009048:2810082-2811255	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	fluoroquinolone
contig00002	28393	29931	emrB	0/0	100.0	98.5	U00096:2812615-2814154	emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin.	fluoroquinolone
contig00005	25955	27010	emrK	0/0	100.0	98.7	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00002	26547	27077	emrR	0/0	100.0	100.0	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00005	24417	25955	emrY	0/0	100.0	98.8	D78168:1591-3130	emrY is a multidrug transport that moves substrates across the inner membrane of the Gram-negative E. coli. It is a homolog of emrB.	tetracycline
contig00024	18418	20061	eptA	0/0	100.0	99.2	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00008	127854	129047	Escherichia_coli_acrA	0/0	100.0	99.8	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00017	92234	93367	Escherichia_coli_ampC	0/0	100.0	97.2	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00005	85287	86591	Escherichia_coli_ampC1_beta-lactamase	0/0	100.0	98.2	FN649414.1:2765050-2766355	An ampC-like beta-lactamase identified from Escherichia coli.	cephalosporin, penam
contig00008	36338	37495	Escherichia_coli_ampH	0/0	100.0	98.7	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig00019	52080	52412	Escherichia_coli_emrE	0/0	100.0	92.2	Z11877.1:485-818	Member of the small MDR (multidrug resistance) family of transporters, in Escherichia coli this protein provides resistance against a number of positively charged compounds including ethidium bromide and erythromycin, proton-dependent secondary transporter which exchanges protons for compound translocation	macrolide
contig00025	30075	31307	Escherichia_coli_mdfA	0/0	100.0	97.6	JQ394987:0-1233	Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter.	benzalkonium_chloride, rhodamine, tetracycline
contig00005	27534	28148	evgA	0/0	100.0	99.0	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00005	28153	31746	evgS	0/0	100.0	99.5	U00096:2484373-2487967	EvgS is a sensor protein that phosphorylates the regulatory protein EvgA. evgS corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	fluoroquinolone, macrolide, penam, tetracycline
contig00006	190476	191204	gadW	0/0	100.0	94.4	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig00006	191572	192396	gadX	0/0	100.0	97.8	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00001	252998	253411	H-NS	0/0	100.0	99.3	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00010	8259	8931	kdpE	0/0	99.3	97.2	U00096.3:721733-721055	kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding.	aminoglycoside
contig00011	56027	56410	marA	0/0	100.0	99.5	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00015	20858	22105	mdtA	0/0	100.0	98.2	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00015	17736	20858	mdtB	0/0	100.0	98.0	U00096:2155262-2158385	MdtB is a transporter that forms a heteromultimer complex with MdtC to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex.	aminocoumarin
contig00015	14658	17735	mdtC	0/0	100.0	98.1	U00096:2158385-2161463	MdtC is a transporter that forms a heteromultimer complex with MdtB to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex. In the absence of MdtB MdtC can form a homomultimer complex that results in a functioning efflux complex with a narrower drug specificity. mdtC corresponds to 3 loci in Pseudomonas aeruginosa PAO1 (gene name: muxC/muxB) and 3 loci in Pseudomonas aeruginosa LESB58.	aminocoumarin
contig00006	185818	186975	mdtE	0/0	100.0	99.7	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00006	187000	190113	mdtF	0/0	100.0	98.6	U00096:3660413-3663527	MdtF is the multidrug inner membrane transporter for the MdtEF-TolC efflux complex.	fluoroquinolone, macrolide, penam
contig00001	462445	463671	mdtG	0/0	100.0	99.2	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00001	452606	453814	mdtH	0/0	100.0	98.8	U00096:1125326-1124117	Multidrug resistance protein MdtH	fluoroquinolone
contig00018	4230	5261	mdtN	0/0	100.0	98.0	AP009048.1:4307588-4306556	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	acridine_dye, nucleoside
contig00018	5261	7312	mdtO	0/0	100.0	98.8	AP009048.1:4306557-4304505	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00018	7309	8775	mdtP	0/0	100.0	98.2	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00005	142312	142788	mphB	0/0	100.0	98.3	AE005174.2:3397370-3397847	The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides.	macrolide
contig00001	598759	600507	msbA	0/0	100.0	99.0	U00096.3:966620-968369	MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability.	nitroimidazole
contig00004	188564	189532	pmrF	0/0	100.0	99.4	U00096:2367070-2368039	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide
contig00004	39588	40244	QnrS1	0/0	100.0	100.0	DQ485529.1:0-657	QnrS1 is a plasmid-mediated quinolone resistance protein found in Shigella flexneri	fluoroquinolone
contig00003	36175	37662	tolC	0/0	100.0	98.4	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan
contig00015	78031	79197	ugd	0/0	100.0	95.9	U00096:2099613-2098446	PmrE is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin	peptide
contig00004	139902	141545	yojI	0/0	100.0	98.2	U00096.3:2308615-2306971	YojI mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. YojI is capable of pumping out microcin molecules. The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI.	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00005	85287	86591	(Bla)AmpC1_Ecoli	0/0	100	98.2	FN649414:2765051-2766355	(Bla)AmpC1_Ecoli	NA
contig00017	92234	93367	(Bla)AmpC2_Ecoli	0/0	100	97.2	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00008	36338	37495	(Bla)ampH_Ecoli	0/0	100	98.7	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00004	34072	34947	(Bla)blaCTX-M-15	0/0	100	100.0	JQ686199:261-1136	(Bla)blaCTX-M-15	NA
contig00010	60720	62621	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100	98.7	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA
contig00004	39588	40244	(Flq)qnr-S1	0/0	100	100.0	AB187515:9737-10393	(Flq)qnr-S1	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00004	34072	34947	blaCTX-M-15	0/0	100	100.0	NG_048935.1	class A extended-spectrum beta-lactamase CTX-M-15	CEPHALOSPORIN
contig00017	92234	93367	blaEC-13	0/0	100	99.6	NG_049079.1	class C extended-spectrum beta-lactamase EC-13	CEPHALOSPORIN
contig00004	39588	40244	qnrS1	0/0	100	100.0	NG_050543.1	quinolone resistance pentapeptide repeat protein QnrS1	QUINOLONE

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00008	127854	129047	ACRA	0/0	100.0	99.8	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00008	124682	127831	ACRB	0/0	100.0	99.1	MEG_401	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRB	NA
contig00005	117709	120822	ACRD	0/0	100.0	98.8	MEG_407	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ACRD	NA
contig00003	270325	271482	ACRE	0/0	100.0	99.0	MEG_408	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRE	NA
contig00003	271494	274598	ACRF	0/0	100.0	99.0	MEG_409	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRF	NA
contig00003	269264	269926	ACRS	0/0	100.0	98.6	MEG_415	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS	NA
contig00008	36338	37495	AMPH	0/0	100.0	98.7	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00015	33712	35564	ASMA	0/0	100.0	98.1	MEG_1180	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:ASMA	NA
contig00003	60021	60840	BACA	0/0	99.8	98.9	MEG_1189	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00015	11123	11845	BAER	0/0	100.0	99.5	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00015	11842	13245	BAES	0/0	100.0	98.7	MEG_1193	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES	NA
contig00004	113440	114630	BCR	0/0	100.0	98.2	MEG_1210	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR	NA
contig00017	92234	93367	BLAEC	0/0	100.0	99.6	MEG_1280	Drugs:betalactams:Class_C_betalactamases:BLAEC	NA
contig00030	21874	22572	CPXAR	0/0	100.0	99.4	MEG_2118	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00030	22569	23942	CPXAR	0/0	100.0	99.1	MEG_2121	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00006	15358	15990	CRP	0/0	100.0	99.2	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00002	27204	28376	EMRA	0/0	100.0	98.2	MEG_2722	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA	NA
contig00002	28393	29931	EMRB	0/0	100.0	98.5	MEG_2725	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRB	NA
contig00013	27804	28994	EMRD	0/0	100.0	99.9	MEG_2729	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD	NA
contig00005	25955	27118	EMRK	0/0	100.0	98.8	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig00002	26547	27077	EMRR	0/0	100.0	100.0	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00005	24417	25955	EMRY	0/0	100.0	98.9	MEG_2736	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRY	NA
contig00024	18418	20061	EPTA	0/0	100.0	99.2	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig00005	28153	31746	EVGS	0/0	100.0	99.5	MEG_2870	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EVGS	NA
contig00006	190476	191204	GADW	0/0	100.0	98.6	MEG_3081	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig00006	191572	192396	GADX	0/0	100.0	97.8	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00001	252998	253411	HNS	0/0	100.0	99.3	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00010	8259	8931	KDPE	0/0	99.3	97.2	MEG_3448	Drugs:Aminoglycosides:Aminoglycoside_efflux_pumps:KDPE	NA
contig00011	56021	56410	MARA	0/0	100.0	99.5	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00011	55573	56007	MARR	0/0	100.0	97.7	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00025	30075	31307	MDFA	0/0	100.0	99.2	MEG_3737	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDFA	NA
contig00015	20858	22105	MDTA	0/0	100.0	98.2	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00015	17736	20858	MDTB	0/0	100.0	98.0	MEG_3747	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTB	NA
contig00015	14658	17735	MDTC	0/0	100.0	98.1	MEG_3749	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTC	NA
contig00006	185818	186975	MDTE	0/0	100.0	99.7	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00006	187000	190113	MDTF	0/0	100.0	98.6	MEG_3752	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTF	NA
contig00001	462445	463671	MDTG	0/0	100.0	99.3	MEG_3753	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig00001	452606	453814	MDTH	0/0	100.0	98.8	MEG_3755	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTH	NA
contig00011	95056	95385	MDTI	0/0	100.0	99.7	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00011	95372	95737	MDTJ	0/0	100.0	98.9	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00007	134591	135964	MDTK	0/0	100.0	99.0	MEG_3759	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:MDTK	NA
contig00018	4230	5261	MDTN	0/0	100.0	98.0	MEG_3763	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN	NA
contig00018	5261	7312	MDTO	0/0	100.0	98.8	MEG_3764	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTO	NA
contig00018	7309	8775	MDTP	0/0	100.0	98.2	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig00005	142312	142788	MPHB	0/0	100.0	98.3	MEG_4033	Drugs:MLS:Macrolide_phosphotransferases:MPHB	NA
contig00001	598759	600507	MSBA	0/0	100.0	99.0	MEG_4061	Drugs:Multi-drug_resistance:Multi-drug_ABC_efflux_pumps:MSBA	NA
contig00019	52080	52412	MVRC	0/0	100.0	92.2	MEG_4103	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MVRC	NA
contig00010	60720	62621	PBP2	0/0	100.0	98.7	MEG_5400	Drugs:betalactams:Penicillin_binding_protein:PBP2	NA
contig00005	85287	86591	PBP4B	0/0	100.0	98.2	MEG_5409	Drugs:betalactams:Penicillin_binding_protein:PBP4B	NA
contig00004	188564	189532	PMRF	0/0	100.0	99.4	MEG_5801	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF	NA
contig00004	39588	40244	QNRS	0/0	100.0	100.0	MEG_6020	Drugs:Fluoroquinolones:Quinolone_resistance_protein_Qnr:QNRS	NA
contig00016	11905	12774	ROBA	0/0	100.0	99.1	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00018	30392	30714	SOXS	0/0	99.7	99.7	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00015	78031	79197	UGD	0/0	100.0	95.9	MEG_7328	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:UGD	NA
contig00004	139902	141545	YOGI	0/0	100.0	98.2	MEG_7842	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:YOGI	NA

ID09CT

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00050	137	925	aadA5_1	0/0	100.0	100	AF137361	aadA5	Streptomycin
contig00015	39907	40782	blaCTX-M-55_1	0/0	100.0	100	DQ810789	blaCTX-M-55	Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig00050	1056	1529	dfrA17_1	0/0	100.0	100	FJ460238	dfrA17	Trimethoprim
contig00004	26129	27361	mdf(A)_1	0/0	100.0	98	Y08743	mdf(A)
contig00044	3600	4256	qnrS1_1	0/0	100.0	100	AB187515	qnrS1	Ciprofloxacin
contig00041	3350	4165	sul2_2	0/0	100.0	100	AY034138	sul2	Sulfamethoxazole
contig00043	3261	4507	tet(A)_6	0/0	97.8	100	AF534183	tet(A)	Doxycycline, Tetracycline

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00050	137	925	aadA5	0/0	100.0	100.0	AF137361:63-852	aadA5 is an aminoglycoside nucleotidyltransferase gene encoded by plasmids transposons and integrons in E. coli K. pneumoniae Kluyvera georgiana P. aeruginosa and E. cloacae	aminoglycoside
contig00024	40300	43449	acrB	0/0	100.0	99.3	U00096.3:484403-481253	Protein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug/proton antiporter.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00001	519811	522924	acrD	0/0	100.0	98.9	AP009048.1:2586250-2589364	AcrD is an aminoglycoside efflux pump expressed in E. coli. Its expression can be induced by indole and is regulated by baeRS and cpxAR.	aminoglycoside
contig00011	138859	140016	acrE	0/0	100.0	99.0	U00096:3413863-3415021	AcrE is a membrane fusion protein similar to AcrA.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00011	140028	143132	acrF	0/0	100.0	98.8	U00096:3415032-3418137	AcrF is a inner membrane transporter similar to AcrB.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00011	137798	138460	acrS	0/0	100.0	99.2	U00096:3413465-3412802	AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.	cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00013	60022	60841	bacA	0/0	99.8	98.9	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00001	129169	129891	baeR	0/0	100.0	99.3	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00001	127769	129172	baeS	0/0	100.0	99.6	AP009048:2165012-2166416	BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.	aminocoumarin, aminoglycoside
contig00022	22408	23781	cpxA	0/0	100.0	98.8	BA000007.3:4905062-4903688	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	aminocoumarin, aminoglycoside
contig00005	15000	15632	CRP	0/0	100.0	99.2	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00015	39907	40782	CTX-M-55	0/0	100.0	100.0	DQ885477:0-876	CTX-M-55 is a beta-lactamase found in the Enterobacteriaceae family	cephalosporin
contig00050	1056	1529	dfrA17	0/0	100.0	100.0	DQ838665:0-474	dfrA17 is an integron-encoded dihydrofolate reductase found in Escherichia coli	diaminopyrimidine
contig00010	58848	60020	emrA	0/0	100.0	98.4	AP009048:2810082-2811255	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	fluoroquinolone
contig00010	60037	61575	emrB	0/0	100.0	99.9	U00096:2812615-2814154	emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin.	fluoroquinolone
contig00001	428091	429146	emrK	0/0	100.0	99.8	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00010	58191	58721	emrR	0/0	100.0	99.6	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00001	426553	428091	emrY	0/0	100.0	99.0	D78168:1591-3130	emrY is a multidrug transport that moves substrates across the inner membrane of the Gram-negative E. coli. It is a homolog of emrB.	tetracycline
contig00026	18390	20033	eptA	0/0	100.0	99.4	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00024	43472	44665	Escherichia_coli_acrA	0/0	100.0	99.8	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00018	98249	99382	Escherichia_coli_ampC	0/0	100.0	97.7	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00001	487410	488714	Escherichia_coli_ampC1_beta-lactamase	0/0	100.0	98.2	FN649414.1:2765050-2766355	An ampC-like beta-lactamase identified from Escherichia coli.	cephalosporin, penam
contig00009	46202	47359	Escherichia_coli_ampH	0/0	100.0	98.8	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig00004	26129	27361	Escherichia_coli_mdfA	0/0	100.0	96.5	JQ394987:0-1233	Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter.	benzalkonium_chloride, rhodamine, tetracycline
contig00001	429670	430284	evgA	0/0	100.0	99.0	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00001	430289	433882	evgS	0/0	100.0	99.4	U00096:2484373-2487967	EvgS is a sensor protein that phosphorylates the regulatory protein EvgA. evgS corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	fluoroquinolone, macrolide, penam, tetracycline
contig00005	184889	185617	gadW	0/0	100.0	94.4	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig00005	185985	186809	gadX	0/0	100.0	97.9	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00003	181458	181871	H-NS	0/0	100.0	99.0	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00012	8052	8724	kdpE	0/0	99.3	97.2	U00096.3:721733-721055	kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding.	aminoglycoside
contig00017	87087	87470	marA	0/0	100.0	99.5	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00001	118909	120156	mdtA	0/0	100.0	98.2	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00001	120156	123278	mdtB	0/0	100.0	98.0	U00096:2155262-2158385	MdtB is a transporter that forms a heteromultimer complex with MdtC to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex.	aminocoumarin
contig00001	123279	126356	mdtC	0/0	100.0	98.1	U00096:2158385-2161463	MdtC is a transporter that forms a heteromultimer complex with MdtB to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex. In the absence of MdtB MdtC can form a homomultimer complex that results in a functioning efflux complex with a narrower drug specificity. mdtC corresponds to 3 loci in Pseudomonas aeruginosa PAO1 (gene name: muxC/muxB) and 3 loci in Pseudomonas aeruginosa LESB58.	aminocoumarin
contig00005	180231	181388	mdtE	0/0	100.0	99.7	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00005	181413	184526	mdtF	0/0	100.0	98.5	U00096:3660413-3663527	MdtF is the multidrug inner membrane transporter for the MdtEF-TolC efflux complex.	fluoroquinolone, macrolide, penam
contig00003	18596	19822	mdtG	0/0	100.0	100.0	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00003	28453	29661	mdtH	0/0	100.0	98.5	U00096:1125326-1124117	Multidrug resistance protein MdtH	fluoroquinolone
contig00019	75674	76906	mdtM	0/0	100.0	96.2	U00096.3:4568519-4567286	Multidrug resistance protein MdtM	acridine_dye, fluoroquinolone, lincosamide, nucleoside, phenicol
contig00020	4247	5278	mdtN	0/0	100.0	97.9	AP009048.1:4307588-4306556	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	acridine_dye, nucleoside
contig00020	5278	7329	mdtO	0/0	100.0	98.4	AP009048.1:4306557-4304505	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00020	7326	8792	mdtP	0/0	100.0	98.2	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00001	544210	544686	mphB	0/0	100.0	98.1	AE005174.2:3397370-3397847	The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides.	macrolide
contig00004	109166	110914	msbA	0/0	100.0	99.0	U00096.3:966620-968369	MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability.	nitroimidazole
contig00001	324356	325324	pmrF	0/0	100.0	99.5	U00096:2367070-2368039	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide
contig00044	3600	4256	QnrS1	0/0	100.0	100.0	DQ485529.1:0-657	QnrS1 is a plasmid-mediated quinolone resistance protein found in Shigella flexneri	fluoroquinolone
contig00041	3350	4165	sul2	0/0	100.0	100.0	AY055428.1:21084-20268	Sul2 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria usually found on small plasmids.	sulfonamide
contig00043	3261	4507	tet(A)	0/0	97.8	100.0	AF534183.1:2970-4245	TetA is a tetracycline efflux pump found in many species of Gram-negative bacteria.	tetracycline
contig00013	36176	37663	tolC	0/0	100.0	98.5	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan
contig00001	275638	277281	yojI	0/0	100.0	98.0	U00096.3:2308615-2306971	YojI mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. YojI is capable of pumping out microcin molecules. The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI.	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00050	137	925	(AGly)aadA5	0/0	100	100.0	AF137361:64-852	(AGly)aadA5	NA
contig00001	487410	488714	(Bla)AmpC1_Ecoli	0/0	100	98.2	FN649414:2765051-2766355	(Bla)AmpC1_Ecoli	NA
contig00018	98249	99382	(Bla)AmpC2_Ecoli	0/0	100	97.7	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00009	46202	47359	(Bla)ampH_Ecoli	0/0	100	98.8	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00015	39907	40782	(Bla)blaCTX-M-55	0/0	100	100.0	HM748991:321-1196	(Bla)blaCTX-M-55	NA
contig00012	60514	62415	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100	98.7	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA
contig00044	3600	4256	(Flq)qnr-S1	0/0	100	100.0	AB187515:9737-10393	(Flq)qnr-S1	NA
contig00041	3350	4165	(Sul)sul2	0/0	100	100.0	EU360945:1617-2432	(Sul)sul2	NA
contig00043	3233	4507	(Tet)tetA	0/0	100	100.0	JX424423:94438-95712	(Tet)tetA	NA
contig00043	4538	5188	(Tet)tetR	0/0	100	99.8	HF545434:53576-54226	(Tet)tetR	NA
contig00050	1056	1529	(Tmt)dfrA17	0/0	100	100.0	AB126604:98-571	(Tmt)dfrA17	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00050	137	925	aadA5	0/0	100	100.0	NG_047357.1	ANT(3’’)-Ia family aminoglycoside nucleotidyltransferase AadA5	STREPTOMYCIN
contig00015	39907	40782	blaCTX-M-55	0/0	100	100.0	NG_049006.1	class A extended-spectrum beta-lactamase CTX-M-55	CEPHALOSPORIN
contig00018	98249	99382	blaEC-18	0/0	100	99.7	NG_049083.1	class C extended-spectrum beta-lactamase EC-18	CEPHALOSPORIN
contig00050	1056	1529	dfrA17	0/0	100	99.8	NG_047710.1	trimethoprim-resistant dihydrofolate reductase DfrA17	TRIMETHOPRIM
contig00044	3600	4256	qnrS1	0/0	100	100.0	NG_050543.1	quinolone resistance pentapeptide repeat protein QnrS1	QUINOLONE
contig00041	3350	4165	sul2	0/0	100	100.0	NG_051852.1	sulfonamide-resistant dihydropteroate synthase Sul2	SULFONAMIDE
contig00043	3233	4432	tet(A)	0/0	100	100.0	NG_048154.1	tetracycline efflux MFS transporter Tet(A)	TETRACYCLINE

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00024	43472	44665	ACRA	0/0	100.0	99.8	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00024	40300	43449	ACRB	0/0	100.0	99.3	MEG_401	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRB	NA
contig00001	519811	522924	ACRD	0/0	100.0	98.9	MEG_407	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ACRD	NA
contig00011	138859	140016	ACRE	0/0	100.0	99.0	MEG_408	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRE	NA
contig00011	140028	143132	ACRF	0/0	100.0	98.8	MEG_409	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRF	NA
contig00011	137798	138460	ACRS	0/0	100.0	99.2	MEG_415	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS	NA
contig00009	46202	47359	AMPH	0/0	100.0	98.8	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00050	137	925	ANT3-DPRIME	0/0	100.0	100.0	MEG_928	Drugs:Aminoglycosides:Aminoglycoside_O-nucleotidyltransferases:ANT3-DPRIME	NA
contig00001	105450	107302	ASMA	0/0	100.0	98.4	MEG_1180	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:ASMA	NA
contig00013	60022	60841	BACA	0/0	99.8	98.9	MEG_1189	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00001	129169	129891	BAER	0/0	100.0	99.3	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00001	127769	129172	BAES	0/0	100.0	99.6	MEG_1193	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES	NA
contig00001	249176	250366	BCR	0/0	100.0	97.5	MEG_1210	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR	NA
contig00018	98249	99382	BLAEC	0/0	100.0	99.7	MEG_1279	Drugs:betalactams:Class_C_betalactamases:BLAEC	NA
contig00022	21713	22411	CPXAR	0/0	100.0	100.0	MEG_2122	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00022	22408	23781	CPXAR	0/0	100.0	99.6	MEG_2121	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00005	15000	15632	CRP	0/0	100.0	99.2	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00050	1056	1529	DFRA	0/0	100.0	100.0	MEG_2547	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00010	58848	60020	EMRA	0/0	100.0	98.4	MEG_2722	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA	NA
contig00010	60037	61575	EMRB	0/0	100.0	99.9	MEG_2725	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRB	NA
contig00006	102812	104002	EMRD	0/0	100.0	99.9	MEG_2729	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD	NA
contig00001	428091	429254	EMRK	0/0	100.0	99.8	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig00010	58191	58721	EMRR	0/0	100.0	99.6	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00001	426553	428091	EMRY	0/0	100.0	99.0	MEG_2736	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRY	NA
contig00026	18390	20033	EPTA	0/0	100.0	99.4	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig00001	430289	433882	EVGS	0/0	100.0	99.4	MEG_2870	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EVGS	NA
contig00005	184889	185617	GADW	0/0	100.0	98.6	MEG_3081	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig00005	185985	186809	GADX	0/0	100.0	97.9	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00003	181458	181871	HNS	0/0	100.0	99.0	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00012	8052	8724	KDPE	0/0	99.3	97.2	MEG_3448	Drugs:Aminoglycosides:Aminoglycoside_efflux_pumps:KDPE	NA
contig00017	87081	87470	MARA	0/0	100.0	99.5	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00017	86633	87067	MARR	0/0	100.0	97.5	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00004	26129	27361	MDFA	0/0	100.0	98.1	MEG_3737	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDFA	NA
contig00001	118909	120156	MDTA	0/0	100.0	98.2	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00001	120156	123278	MDTB	0/0	100.0	98.0	MEG_3747	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTB	NA
contig00001	123279	126356	MDTC	0/0	100.0	98.1	MEG_3749	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTC	NA
contig00005	180231	181388	MDTE	0/0	100.0	99.7	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00005	181413	184526	MDTF	0/0	100.0	98.5	MEG_3752	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTF	NA
contig00003	18596	19822	MDTG	0/0	100.0	100.0	MEG_3754	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig00003	28453	29661	MDTH	0/0	100.0	98.5	MEG_3755	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTH	NA
contig00002	377430	377759	MDTI	0/0	100.0	99.4	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00002	377078	377443	MDTJ	0/0	100.0	99.7	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00002	305939	307312	MDTK	0/0	100.0	99.0	MEG_3759	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:MDTK	NA
contig00019	75674	76906	MDTM	0/0	100.0	96.2	MEG_3761	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTM	NA
contig00020	4247	5278	MDTN	0/0	100.0	97.9	MEG_3763	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN	NA
contig00020	5278	7329	MDTO	0/0	100.0	98.4	MEG_3764	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTO	NA
contig00020	7326	8792	MDTP	0/0	100.0	98.2	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig00001	544210	544686	MPHB	0/0	100.0	98.1	MEG_4033	Drugs:MLS:Macrolide_phosphotransferases:MPHB	NA
contig00004	109166	110914	MSBA	0/0	100.0	99.0	MEG_4061	Drugs:Multi-drug_resistance:Multi-drug_ABC_efflux_pumps:MSBA	NA
contig00012	60514	62415	PBP2	0/0	100.0	98.7	MEG_5400	Drugs:betalactams:Penicillin_binding_protein:PBP2	NA
contig00001	487410	488714	PBP4B	0/0	100.0	98.2	MEG_5409	Drugs:betalactams:Penicillin_binding_protein:PBP4B	NA
contig00001	324356	325324	PMRF	0/0	100.0	99.5	MEG_5801	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF	NA
contig00044	3600	4256	QNRS	0/0	100.0	100.0	MEG_6020	Drugs:Fluoroquinolones:Quinolone_resistance_protein_Qnr:QNRS	NA
contig00019	11911	12780	ROBA	0/0	100.0	99.1	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00020	30407	30730	SOXS	0/0	100.0	99.7	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00041	3350	4165	SULII	0/0	100.0	100.0	MEG_6617	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULII	NA
contig00043	3233	4507	TETA	0/0	100.0	100.0	MEG_7024	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETA	NA
contig00001	275638	277281	YOGI	0/0	100.0	98.0	MEG_7842	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:YOGI	NA

ID101

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00003	231391	232266	blaCTX-M-15_1	0/0	100	100.0	AY044436	blaCTX-M-15	Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig00021	30102	31334	mdf(A)_1	0/0	100	99.1	Y08743	mdf(A)
contig00003	226094	226750	qnrS1_1	0/0	100	100.0	AB187515	qnrS1	Ciprofloxacin

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00011	124682	127831	acrB	0/0	100.0	99.1	U00096.3:484403-481253	Protein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug/proton antiporter.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00005	117709	120822	acrD	0/0	100.0	98.8	AP009048.1:2586250-2589364	AcrD is an aminoglycoside efflux pump expressed in E. coli. Its expression can be induced by indole and is regulated by baeRS and cpxAR.	aminoglycoside
contig00004	270325	271482	acrE	0/0	100.0	99.0	U00096:3413863-3415021	AcrE is a membrane fusion protein similar to AcrA.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00004	271494	274598	acrF	0/0	100.0	99.0	U00096:3415032-3418137	AcrF is a inner membrane transporter similar to AcrB.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00004	269264	269926	acrS	0/0	100.0	98.6	U00096:3413465-3412802	AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.	cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00004	60021	60840	bacA	0/0	99.8	98.7	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00003	277506	278228	baeR	0/0	100.0	99.5	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00003	278225	279628	baeS	0/0	100.0	98.7	AP009048:2165012-2166416	BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.	aminocoumarin, aminoglycoside
contig00038	22569	23942	cpxA	0/0	100.0	98.5	BA000007.3:4905062-4903688	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	aminocoumarin, aminoglycoside
contig00007	15000	15632	CRP	0/0	100.0	99.2	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00003	231391	232266	CTX-M-15	0/0	100.0	100.0	AY044436:1435-2311	CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family	cephalosporin
contig00002	27204	28376	emrA	0/0	100.0	98.2	AP009048:2810082-2811255	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	fluoroquinolone
contig00002	28393	29931	emrB	0/0	100.0	98.5	U00096:2812615-2814154	emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin.	fluoroquinolone
contig00005	25955	27010	emrK	0/0	100.0	98.7	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00002	26547	27077	emrR	0/0	100.0	100.0	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00005	24417	25955	emrY	0/0	100.0	98.8	D78168:1591-3130	emrY is a multidrug transport that moves substrates across the inner membrane of the Gram-negative E. coli. It is a homolog of emrB.	tetracycline
contig00012	115182	116825	eptA	0/0	100.0	99.2	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00011	127854	129047	Escherichia_coli_acrA	0/0	100.0	99.8	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00022	50255	51388	Escherichia_coli_ampC	0/0	100.0	97.2	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00005	85287	86591	Escherichia_coli_ampC1_beta-lactamase	0/0	100.0	98.2	FN649414.1:2765050-2766355	An ampC-like beta-lactamase identified from Escherichia coli.	cephalosporin, penam
contig00011	36338	37495	Escherichia_coli_ampH	0/0	100.0	98.7	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig00029	3730	4062	Escherichia_coli_emrE	0/0	100.0	92.2	Z11877.1:485-818	Member of the small MDR (multidrug resistance) family of transporters, in Escherichia coli this protein provides resistance against a number of positively charged compounds including ethidium bromide and erythromycin, proton-dependent secondary transporter which exchanges protons for compound translocation	macrolide
contig00021	30102	31334	Escherichia_coli_mdfA	0/0	100.0	97.6	JQ394987:0-1233	Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter.	benzalkonium_chloride, rhodamine, tetracycline
contig00005	27534	28148	evgA	0/0	100.0	99.0	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00005	28153	31746	evgS	0/0	100.0	99.5	U00096:2484373-2487967	EvgS is a sensor protein that phosphorylates the regulatory protein EvgA. evgS corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	fluoroquinolone, macrolide, penam, tetracycline
contig00007	190118	190846	gadW	0/0	100.0	94.4	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig00007	191214	192038	gadX	0/0	100.0	97.8	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00001	69273	69686	H-NS	0/0	100.0	99.3	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00008	9078	9750	kdpE	0/0	99.3	97.2	U00096.3:721733-721055	kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding.	aminoglycoside
contig00014	56027	56410	marA	0/0	100.0	99.5	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00003	287241	288488	mdtA	0/0	100.0	98.2	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00003	284119	287241	mdtB	0/0	100.0	98.0	U00096:2155262-2158385	MdtB is a transporter that forms a heteromultimer complex with MdtC to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex.	aminocoumarin
contig00003	281041	284118	mdtC	0/0	100.0	98.1	U00096:2158385-2161463	MdtC is a transporter that forms a heteromultimer complex with MdtB to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex. In the absence of MdtB MdtC can form a homomultimer complex that results in a functioning efflux complex with a narrower drug specificity. mdtC corresponds to 3 loci in Pseudomonas aeruginosa PAO1 (gene name: muxC/muxB) and 3 loci in Pseudomonas aeruginosa LESB58.	aminocoumarin
contig00007	185460	186617	mdtE	0/0	100.0	99.7	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00007	186642	189755	mdtF	0/0	100.0	98.6	U00096:3660413-3663527	MdtF is the multidrug inner membrane transporter for the MdtEF-TolC efflux complex.	fluoroquinolone, macrolide, penam
contig00001	278720	279946	mdtG	0/0	100.0	99.2	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00001	268881	270089	mdtH	0/0	100.0	98.8	U00096:1125326-1124117	Multidrug resistance protein MdtH	fluoroquinolone
contig00012	91422	92453	mdtN	0/0	100.0	98.0	AP009048.1:4307588-4306556	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	acridine_dye, nucleoside
contig00012	89371	91422	mdtO	0/0	100.0	98.8	AP009048.1:4306557-4304505	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00012	87908	89374	mdtP	0/0	100.0	98.2	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00005	142312	142788	mphB	0/0	100.0	98.3	AE005174.2:3397370-3397847	The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides.	macrolide
contig00001	415034	416782	msbA	0/0	100.0	99.0	U00096.3:966620-968369	MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability.	nitroimidazole
contig00003	76806	77774	pmrF	0/0	100.0	99.4	U00096:2367070-2368039	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide
contig00003	226094	226750	QnrS1	0/0	100.0	100.0	DQ485529.1:0-657	QnrS1 is a plasmid-mediated quinolone resistance protein found in Shigella flexneri	fluoroquinolone
contig00004	36175	37662	tolC	0/0	100.0	98.4	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan
contig00003	344414	345580	ugd	0/0	100.0	95.9	U00096:2099613-2098446	PmrE is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin	peptide
contig00003	124793	126436	yojI	0/0	100.0	98.2	U00096.3:2308615-2306971	YojI mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. YojI is capable of pumping out microcin molecules. The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI.	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00005	85287	86591	(Bla)AmpC1_Ecoli	0/0	100	98.2	FN649414:2765051-2766355	(Bla)AmpC1_Ecoli	NA
contig00022	50255	51388	(Bla)AmpC2_Ecoli	0/0	100	97.2	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00011	36338	37495	(Bla)ampH_Ecoli	0/0	100	98.7	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00003	231391	232266	(Bla)blaCTX-M-15	0/0	100	100.0	JQ686199:261-1136	(Bla)blaCTX-M-15	NA
contig00008	61539	63440	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100	98.7	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA
contig00003	226094	226750	(Flq)qnr-S1	0/0	100	100.0	AB187515:9737-10393	(Flq)qnr-S1	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00003	231391	232266	blaCTX-M-15	0/0	100	100.0	NG_048935.1	class A extended-spectrum beta-lactamase CTX-M-15	CEPHALOSPORIN
contig00022	50255	51388	blaEC-13	0/0	100	99.6	NG_049079.1	class C extended-spectrum beta-lactamase EC-13	CEPHALOSPORIN
contig00003	226094	226750	qnrS1	0/0	100	100.0	NG_050543.1	quinolone resistance pentapeptide repeat protein QnrS1	QUINOLONE

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00011	127854	129047	ACRA	0/0	100.0	99.8	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00011	124682	127831	ACRB	0/0	100.0	99.1	MEG_401	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRB	NA
contig00005	117709	120822	ACRD	0/0	100.0	98.8	MEG_407	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ACRD	NA
contig00004	270325	271482	ACRE	0/0	100.0	99.0	MEG_408	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRE	NA
contig00004	271494	274598	ACRF	0/0	100.0	99.0	MEG_409	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRF	NA
contig00004	269264	269926	ACRS	0/0	100.0	98.6	MEG_415	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS	NA
contig00011	36338	37495	AMPH	0/0	100.0	98.7	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00003	300095	301947	ASMA	0/0	100.0	98.1	MEG_1180	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:ASMA	NA
contig00004	60021	60840	BACA	0/0	99.8	98.9	MEG_1189	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00003	277506	278228	BAER	0/0	100.0	99.5	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00003	278225	279628	BAES	0/0	100.0	98.7	MEG_1193	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES	NA
contig00003	151708	152898	BCR	0/0	100.0	98.2	MEG_1210	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR	NA
contig00022	50255	51388	BLAEC	0/0	100.0	99.6	MEG_1280	Drugs:betalactams:Class_C_betalactamases:BLAEC	NA
contig00038	21874	22572	CPXAR	0/0	100.0	99.4	MEG_2118	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00038	22569	23942	CPXAR	0/0	100.0	99.1	MEG_2121	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00007	15000	15632	CRP	0/0	100.0	99.2	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00002	27204	28376	EMRA	0/0	100.0	98.2	MEG_2722	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA	NA
contig00002	28393	29931	EMRB	0/0	100.0	98.5	MEG_2725	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRB	NA
contig00016	27804	28994	EMRD	0/0	100.0	99.9	MEG_2729	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD	NA
contig00005	25955	27118	EMRK	0/0	100.0	98.8	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig00002	26547	27077	EMRR	0/0	100.0	100.0	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00005	24417	25955	EMRY	0/0	100.0	98.9	MEG_2736	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRY	NA
contig00012	115182	116825	EPTA	0/0	100.0	99.2	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig00005	28153	31746	EVGS	0/0	100.0	99.5	MEG_2870	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EVGS	NA
contig00007	190118	190846	GADW	0/0	100.0	98.6	MEG_3081	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig00007	191214	192038	GADX	0/0	100.0	97.8	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00001	69273	69686	HNS	0/0	100.0	99.3	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00008	9078	9750	KDPE	0/0	99.3	97.2	MEG_3448	Drugs:Aminoglycosides:Aminoglycoside_efflux_pumps:KDPE	NA
contig00014	56021	56410	MARA	0/0	100.0	99.5	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00014	55573	56007	MARR	0/0	100.0	97.7	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00021	30102	31334	MDFA	0/0	100.0	99.2	MEG_3737	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDFA	NA
contig00003	287241	288488	MDTA	0/0	100.0	98.2	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00003	284119	287241	MDTB	0/0	100.0	98.0	MEG_3747	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTB	NA
contig00003	281041	284118	MDTC	0/0	100.0	98.1	MEG_3749	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTC	NA
contig00007	185460	186617	MDTE	0/0	100.0	99.7	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00007	186642	189755	MDTF	0/0	100.0	98.6	MEG_3752	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTF	NA
contig00001	278720	279946	MDTG	0/0	100.0	99.3	MEG_3753	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig00001	268881	270089	MDTH	0/0	100.0	98.8	MEG_3755	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTH	NA
contig00014	95056	95385	MDTI	0/0	100.0	99.7	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00014	95372	95737	MDTJ	0/0	100.0	98.9	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00010	134591	135964	MDTK	0/0	100.0	99.0	MEG_3759	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:MDTK	NA
contig00012	91422	92453	MDTN	0/0	100.0	98.0	MEG_3763	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN	NA
contig00012	89371	91422	MDTO	0/0	100.0	98.8	MEG_3764	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTO	NA
contig00012	87908	89374	MDTP	0/0	100.0	98.2	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig00005	142312	142788	MPHB	0/0	100.0	98.3	MEG_4033	Drugs:MLS:Macrolide_phosphotransferases:MPHB	NA
contig00001	415034	416782	MSBA	0/0	100.0	99.0	MEG_4061	Drugs:Multi-drug_resistance:Multi-drug_ABC_efflux_pumps:MSBA	NA
contig00029	3730	4062	MVRC	0/0	100.0	92.2	MEG_4103	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MVRC	NA
contig00008	61539	63440	PBP2	0/0	100.0	98.7	MEG_5400	Drugs:betalactams:Penicillin_binding_protein:PBP2	NA
contig00005	85287	86591	PBP4B	0/0	100.0	98.2	MEG_5409	Drugs:betalactams:Penicillin_binding_protein:PBP4B	NA
contig00003	76806	77774	PMRF	0/0	100.0	99.4	MEG_5801	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF	NA
contig00003	226094	226750	QNRS	0/0	100.0	100.0	MEG_6020	Drugs:Fluoroquinolones:Quinolone_resistance_protein_Qnr:QNRS	NA
contig00018	11905	12774	ROBA	0/0	100.0	99.1	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00012	65969	66291	SOXS	0/0	99.7	99.7	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00003	344414	345580	UGD	0/0	100.0	95.9	MEG_7328	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:UGD	NA
contig00003	124793	126436	YOGI	0/0	100.0	98.2	MEG_7842	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:YOGI	NA

ID107II

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00103	1694	2554	aac(3)-IIa_1	0/0	100	99.8	X51534	aac(3)-IIa	Gentamicin, Tobramycin
contig00108	1539	2138	aac(6’)-Ib-cr_1	0/0	100	100.0	DQ303918	aac(6’)-Ib-cr	Ciprofloxacin
contig00076	1442	2230	aadA5_1	0/0	100	100.0	AF137361	aadA5	Streptomycin
contig00060	5615	6418	aph(3’’)-Ib_5	0/0	100	100.0	AF321551	aph(3’’)-Ib	Streptomycin
contig00060	4779	5615	aph(6)-Id_1	0/0	100	99.9	M28829	aph(6)-Id	Streptomycin
contig00058	6763	7638	blaCTX-M-15_1	0/0	100	100.0	AY044436	blaCTX-M-15	Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig00108	578	1408	blaOXA-1_1	0/0	100	100.0	HQ170510	blaOXA-1	Amoxicillin, Amoxicillin+Clavulanic_acid, Ampicillin, Ampicillin+Clavulanic_acid, Cefepime, Piperacillin, Piperacillin+Tazobactam
contig00060	8797	9657	blaTEM-1B_1	0/0	100	100.0	AY458016	blaTEM-1B	Amoxicillin, Ampicillin, Cephalothin, Piperacillin, Ticarcillin
contig00086	223	882	catA1_1	0/0	100	99.8	V00622	catA1	Chloramphenicol
contig00076	838	1311	dfrA17_1	0/0	100	100.0	FJ460238	dfrA17	Trimethoprim
contig00124	42	551	dfrA8_1	0/0	100	100.0	U10186	dfrA8	Trimethoprim
contig00001	66890	68122	mdf(A)_1	0/0	100	98.3	Y08743	mdf(A)
contig00076	2750	3616	sul1_5	0/0	100	99.9	EU780013	sul1	Sulfamethoxazole
contig00060	6479	7294	sul2_2	0/0	100	100.0	AY034138	sul2	Sulfamethoxazole
contig00090	1009	2214	tet(B)_2	0/0	100	100.0	AF326777	tet(B)	Doxycycline, Tetracycline, Minocycline

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00103	1694	2554	AAC(3)-IIe	0/0	100.0	99.5	EU022315.1:0-861	AAC(3)-IIe is a plasmid-encoded aminoglycoside acetyltransferase in E. coli	aminoglycoside
contig00108	1539	2138	AAC(6’)-Ib-cr	0/0	100.0	100.0	DQ303918:0-600	AAC(6’)-Ib-cr is an aminoglycoside acetyltransferase encoded by plasmids transposons integrons in Enterobacteriaceae. The aac(6’)-Ib-cr variant gene can induce resistance against aminoglycoside and fluoroquinolone simultaneously	aminoglycoside, fluoroquinolone
contig00076	1442	2230	aadA5	0/0	100.0	100.0	AF137361:63-852	aadA5 is an aminoglycoside nucleotidyltransferase gene encoded by plasmids transposons and integrons in E. coli K. pneumoniae Kluyvera georgiana P. aeruginosa and E. cloacae	aminoglycoside
contig00006	83264	86413	acrB	0/0	100.0	99.0	U00096.3:484403-481253	Protein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug/proton antiporter.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00002	166193	169306	acrD	0/0	100.0	98.7	AP009048.1:2586250-2589364	AcrD is an aminoglycoside efflux pump expressed in E. coli. Its expression can be induced by indole and is regulated by baeRS and cpxAR.	aminoglycoside
contig00012	8666	9823	acrE	0/0	100.0	98.2	U00096:3413863-3415021	AcrE is a membrane fusion protein similar to AcrA.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00012	5550	8654	acrF	0/0	100.0	97.5	U00096:3415032-3418137	AcrF is a inner membrane transporter similar to AcrB.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00012	10222	10884	acrS	0/0	100.0	97.6	U00096:3413465-3412802	AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.	cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00060	5615	6418	APH(3’’)-Ib	0/0	100.0	99.8	AF313472:15593-16397	APH(3’’)-Ib is an aminoglycoside phosphotransferase encoded by plasmids transposons integrative conjugative elements and chromosomes in Enterobacteriaceae and Pseudomonas spp.	aminoglycoside
contig00060	4779	5615	APH(6)-Id	0/0	100.0	99.8	AF024602:3155-3992	APH(6)-Id is an aminoglycoside phosphotransferase encoded by plasmids integrative conjugative elements and chromosomal genomic islands in K. pneumoniae Salmonella spp. E. coli Shigella flexneri Providencia alcalifaciens Pseudomonas spp. V. cholerae Edwardsiella tarda Pasteurella multocida and Aeromonas bestiarum	aminoglycoside
contig00010	75623	76442	bacA	0/0	99.8	97.0	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00039	9386	10107	baeR	0/0	99.9	97.0	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00039	10104	11507	baeS	0/0	100.0	92.2	AP009048:2165012-2166416	BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.	aminocoumarin, aminoglycoside
contig00086	223	882	catI	0/0	100.0	99.8	V00622:243-903	catI is a chromosome and transposon-encoded variant of the cat gene found in Escherichia coli and Acinetobacter baumannii	phenicol
contig00036	22665	24038	cpxA	0/0	100.0	98.9	BA000007.3:4905062-4903688	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	aminocoumarin, aminoglycoside
contig00007	15337	15969	CRP	0/0	100.0	99.2	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00058	6763	7638	CTX-M-15	0/0	100.0	100.0	AY044436:1435-2311	CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family	cephalosporin
contig00076	838	1311	dfrA17	0/0	100.0	100.0	DQ838665:0-474	dfrA17 is an integron-encoded dihydrofolate reductase found in Escherichia coli	diaminopyrimidine
contig00124	42	551	dfrA8	0/0	100.0	100.0	KJ174469:710-1220	dfrA8 is a transposon-encoded dihydrofolate reductase found in Salmonella enterica	diaminopyrimidine
contig00014	54859	56031	emrA	0/0	100.0	98.1	AP009048:2810082-2811255	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	fluoroquinolone
contig00014	56048	57586	emrB	0/0	100.0	98.5	U00096:2812615-2814154	emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin.	fluoroquinolone
contig00002	68336	69391	emrK	0/0	100.0	96.9	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00014	54202	54732	emrR	0/0	100.0	99.4	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00002	66798	68336	emrY	0/0	100.0	98.0	D78168:1591-3130	emrY is a multidrug transport that moves substrates across the inner membrane of the Gram-negative E. coli. It is a homolog of emrB.	tetracycline
contig00026	22597	24240	eptA	0/0	100.0	98.2	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00006	82048	83241	Escherichia_coli_acrA	0/0	100.0	99.0	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00011	118247	119380	Escherichia_coli_ampC	0/0	100.0	98.1	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00002	131660	132964	Escherichia_coli_ampC1_beta-lactamase	0/0	100.0	95.2	FN649414.1:2765050-2766355	An ampC-like beta-lactamase identified from Escherichia coli.	cephalosporin, penam
contig00006	172662	173819	Escherichia_coli_ampH	0/0	100.0	97.3	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig00035	21833	22165	Escherichia_coli_emrE	0/0	100.0	91.9	Z11877.1:485-818	Member of the small MDR (multidrug resistance) family of transporters, in Escherichia coli this protein provides resistance against a number of positively charged compounds including ethidium bromide and erythromycin, proton-dependent secondary transporter which exchanges protons for compound translocation	macrolide
contig00001	66890	68122	Escherichia_coli_mdfA	0/0	100.0	96.8	JQ394987:0-1233	Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter.	benzalkonium_chloride, rhodamine, tetracycline
contig00002	69914	70528	evgA	0/0	100.0	99.3	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00002	70533	74126	evgS	0/0	100.0	96.6	U00096:2484373-2487967	EvgS is a sensor protein that phosphorylates the regulatory protein EvgA. evgS corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	fluoroquinolone, macrolide, penam, tetracycline
contig00007	194554	195282	gadW	0/0	100.0	95.9	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig00007	195651	196475	gadX	0/0	100.0	93.9	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00025	51443	51856	H-NS	0/0	100.0	99.5	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00001	245399	246076	kdpE	0/0	100.0	95.6	U00096.3:721733-721055	kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding.	aminoglycoside
contig00031	27852	28235	marA	0/0	100.0	100.0	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00039	19120	20367	mdtA	0/0	100.0	96.5	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00039	15998	19120	mdtB	0/0	100.0	96.9	U00096:2155262-2158385	MdtB is a transporter that forms a heteromultimer complex with MdtC to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex.	aminocoumarin
contig00039	12920	15997	mdtC	0/0	100.0	96.7	U00096:2158385-2161463	MdtC is a transporter that forms a heteromultimer complex with MdtB to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex. In the absence of MdtB MdtC can form a homomultimer complex that results in a functioning efflux complex with a narrower drug specificity. mdtC corresponds to 3 loci in Pseudomonas aeruginosa PAO1 (gene name: muxC/muxB) and 3 loci in Pseudomonas aeruginosa LESB58.	aminocoumarin
contig00007	189896	191053	mdtE	0/0	100.0	99.0	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00007	191078	194191	mdtF	0/0	100.0	98.4	U00096:3660413-3663527	MdtF is the multidrug inner membrane transporter for the MdtEF-TolC efflux complex.	fluoroquinolone, macrolide, penam
contig00004	186815	188041	mdtG	0/0	100.0	98.3	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00004	196672	197880	mdtH	0/0	100.0	98.0	U00096:1125326-1124117	Multidrug resistance protein MdtH	fluoroquinolone
contig00003	320318	321550	mdtM	0/0	100.0	100.0	U00096.3:4568519-4567286	Multidrug resistance protein MdtM	acridine_dye, fluoroquinolone, lincosamide, nucleoside, phenicol
contig00023	6589	7620	mdtN	0/0	100.0	97.7	AP009048.1:4307588-4306556	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	acridine_dye, nucleoside
contig00023	7620	9671	mdtO	0/0	100.0	96.6	AP009048.1:4306557-4304505	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00023	9668	11134	mdtP	0/0	100.0	96.5	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00002	190013	190487	mphB	0/0	99.6	96.2	AE005174.2:3397370-3397847	The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides.	macrolide
contig00004	52279	54027	msbA	0/0	100.0	98.9	U00096.3:966620-968369	MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability.	nitroimidazole
contig00108	578	1408	OXA-1	0/0	100.0	100.0	JN420336.1:2230-1399	OXA-1 is a beta-lactamase found in E. coli	cephalosporin, penam
contig00037	1872	2840	pmrF	0/0	100.0	97.9	U00096:2367070-2368039	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide
contig00076	2777	3616	sul1	0/0	100.0	100.0	JF969163:1053-1893	Sul1 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria. It is linked to other resistance genes of class 1 integrons.	sulfonamide
contig00060	6479	7294	sul2	0/0	100.0	100.0	AY055428.1:21084-20268	Sul2 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria usually found on small plasmids.	sulfonamide
contig00060	8797	9657	TEM-1	0/0	100.0	99.9	AL513383:161910-162771	TEM-1 is a broad-spectrum beta-lactamase found in many Gram-negative bacteria. Confers resistance to penicillins and first generation cephalosphorins.	cephalosporin, monobactam, penam, penem
contig00090	1009	2214	tet(B)	0/0	100.0	99.8	AB089595:0-1206	Tet(B) is a tetracycline efflux protein expressed in many Gram-negative bacteria. It confers resistance to tetracycline doxycycline and minocycline but not tigecycline.	tetracycline
contig00010	53808	55295	tolC	0/0	100.0	97.9	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan
contig00019	31242	32408	ugd	0/0	100.0	96.9	U00096:2099613-2098446	PmrE is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin	peptide
contig00013	75473	77116	yojI	0/0	100.0	97.8	U00096.3:2308615-2306971	YojI mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. YojI is capable of pumping out microcin molecules. The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI.	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00103	1694	2554	(AGly)aac3-IIa	0/0	100	99.8	X51534:91-951	(AGly)aac3-IIa	NA
contig00076	1442	2230	(AGly)aadA5	0/0	100	100.0	AF137361:64-852	(AGly)aadA5	NA
contig00060	5615	6418	(AGly)strA	0/0	100	99.9	AB366441:22458-23261	(AGly)strA	NA
contig00060	4779	5615	(AGly)strB	0/0	100	99.9	FJ474091:264-1100	(AGly)strB	NA
contig00002	131660	132964	(Bla)AmpC1_Ecoli	0/0	100	95.2	FN649414:2765051-2766355	(Bla)AmpC1_Ecoli	NA
contig00011	118247	119380	(Bla)AmpC2_Ecoli	0/0	100	98.1	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00006	172662	173819	(Bla)ampH_Ecoli	0/0	100	97.3	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00058	6763	7638	(Bla)blaCTX-M-15	0/0	100	100.0	JQ686199:261-1136	(Bla)blaCTX-M-15	NA
contig00108	578	1408	(Bla)blaOXA-1	0/0	100	100.0	JQ682867:1-831	(Bla)blaOXA-1	NA
contig00060	8797	9657	(Bla)blaTEM-105	0/0	100	99.9	AF516720:215-1075	(Bla)blaTEM-105	NA
contig00001	299932	301833	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100	98.4	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA
contig00086	223	882	(Phe)catA1	0/0	100	99.8	V00622:244-903	(Phe)catA1	NA
contig00076	2777	3616	(Sul)sul1	0/0	100	100.0	AF071413:6700-7539	(Sul)sul1	NA
contig00060	6479	7294	(Sul)sul2	0/0	100	100.0	EU360945:1617-2432	(Sul)sul2	NA
contig00090	1009	2214	(Tet)tetB	0/0	100	99.7	AB089594:1-1206	(Tet)tetB	NA
contig00076	838	1311	(Tmt)dfrA17	0/0	100	100.0	AB126604:98-571	(Tmt)dfrA17	NA
contig00124	42	551	(Tmt)dfrA8	0/0	100	100.0	U10186:711-1220	(Tmt)dfrA8	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00103	1694	2554	aac(3)-IIe	0/0	100	99.8	NG_047244.1	aminoglycoside N-acetyltransferase AAC(3)-IIe	GENTAMICIN
contig00108	1539	2093	aac(6’)-Ib-D181Y	0/0	100	99.8	NG_067946.1	AAC(6’)-Ib family aminoglycoside 6’-N-acetyltransferase	AMIKACIN, KANAMYCIN, TOBRAMYCIN
contig00076	1442	2230	aadA5	0/0	100	100.0	NG_047357.1	ANT(3’’)-Ia family aminoglycoside nucleotidyltransferase AadA5	STREPTOMYCIN
contig00060	5615	6442	aph(3’’)-Ib	0/0	100	100.0	NG_056002.2	aminoglycoside O-phosphotransferase APH(3’’)-Ib	STREPTOMYCIN
contig00060	4779	5615	aph(6)-Id	0/0	100	100.0	NG_047466.1	aminoglycoside O-phosphotransferase APH(6)-Id	STREPTOMYCIN
contig00058	6763	7638	blaCTX-M-15	0/0	100	100.0	NG_048935.1	class A extended-spectrum beta-lactamase CTX-M-15	CEPHALOSPORIN
contig00011	118247	119380	blaEC-19	0/0	100	99.9	NG_049084.1	class C extended-spectrum beta-lactamase EC-19	CEPHALOSPORIN
contig00108	578	1408	blaOXA-1	0/0	100	100.0	NG_049392.1	oxacillin-hydrolyzing class D beta-lactamase OXA-1	CEPHALOSPORIN
contig00060	8797	9657	blaTEM-1	0/0	100	100.0	NG_050145.1	class A broad-spectrum beta-lactamase TEM-1	BETA-LACTAM
contig00086	223	882	catA1	0/0	100	99.8	NG_047582.1	type A-1 chloramphenicol O-acetyltransferase	CHLORAMPHENICOL
contig00076	838	1311	dfrA17	0/0	100	99.8	NG_047710.1	trimethoprim-resistant dihydrofolate reductase DfrA17	TRIMETHOPRIM
contig00124	42	551	dfrA8	0/0	100	100.0	NG_047741.1	trimethoprim-resistant dihydrofolate reductase DfrA8	TRIMETHOPRIM
contig00076	2777	3616	sul1	0/0	100	100.0	NG_048082.1	sulfonamide-resistant dihydropteroate synthase Sul1	SULFONAMIDE
contig00060	6479	7294	sul2	0/0	100	100.0	NG_051852.1	sulfonamide-resistant dihydropteroate synthase Sul2	SULFONAMIDE
contig00090	1009	2214	tet(B)	0/0	100	100.0	NG_048163.1	tetracycline efflux MFS transporter Tet(B)	TETRACYCLINE

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00103	1694	2554	AAC3	0/0	100.0	99.8	MEG_44	Drugs:Aminoglycosides:Aminoglycoside_N-acetyltransferases:AAC3	NA
contig00006	82048	83241	ACRA	0/0	100.0	99.0	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00006	83264	86413	ACRB	0/0	100.0	99.0	MEG_401	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRB	NA
contig00002	166193	169306	ACRD	0/0	100.0	98.7	MEG_407	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ACRD	NA
contig00012	8666	9823	ACRE	0/0	100.0	98.2	MEG_408	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRE	NA
contig00012	5550	8654	ACRF	0/0	100.0	97.5	MEG_409	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRF	NA
contig00012	10222	10884	ACRS	0/0	100.0	97.6	MEG_415	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS	NA
contig00006	172662	173819	AMPH	0/0	100.0	97.3	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00076	1442	2230	ANT3-DPRIME	0/0	100.0	100.0	MEG_928	Drugs:Aminoglycosides:Aminoglycoside_O-nucleotidyltransferases:ANT3-DPRIME	NA
contig00060	5615	6442	APH3-DPRIME	0/0	100.0	100.0	MEG_1019	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH3-DPRIME	NA
contig00060	4779	5615	APH6	0/0	100.0	100.0	MEG_1084	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH6	NA
contig00039	31975	33828	ASMA	0/0	100.0	97.8	MEG_1180	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:ASMA	NA
contig00010	75623	76442	BACA	0/0	99.8	97.2	MEG_1189	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00039	9386	10107	BAER	0/0	99.9	97.0	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00039	10104	11507	BAES	0/0	100.0	92.2	MEG_1193	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES	NA
contig00013	49010	50200	BCR	0/0	100.0	96.6	MEG_1210	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR	NA
contig00011	118247	119380	BLAEC	0/0	100.0	99.9	MEG_1277	Drugs:betalactams:Class_C_betalactamases:BLAEC	NA
contig00086	212	882	CATA	0/0	100.0	100.0	MEG_1593	Drugs:Phenicol:Chloramphenicol_acetyltransferases:CATA	NA
contig00036	21970	22668	CPXAR	0/0	100.0	99.4	MEG_2118	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00036	22665	24038	CPXAR	0/0	100.0	99.0	MEG_2121	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00007	15337	15969	CRP	0/0	100.0	99.2	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00076	838	1311	DFRA	0/0	100.0	100.0	MEG_2547	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00124	42	551	DFRA	0/0	100.0	100.0	MEG_2553	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00014	54859	56031	EMRA	0/0	100.0	98.1	MEG_2722	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA	NA
contig00014	56048	57586	EMRB	0/0	100.0	98.5	MEG_2725	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRB	NA
contig00015	89483	90673	EMRD	0/0	100.0	97.8	MEG_2729	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD	NA
contig00002	68336	69499	EMRK	0/0	100.0	96.7	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig00014	54202	54732	EMRR	0/0	100.0	99.4	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00002	66798	68336	EMRY	0/0	100.0	98.1	MEG_2736	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRY	NA
contig00026	22597	24240	EPTA	0/0	100.0	98.2	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig00002	70533	74126	EVGS	0/0	100.0	97.1	MEG_2869	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EVGS	NA
contig00007	194554	195282	GADW	0/0	100.0	97.0	MEG_3081	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig00007	195651	196475	GADX	0/0	100.0	93.9	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00025	51443	51856	HNS	0/0	100.0	99.5	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00001	245399	246076	KDPE	0/0	100.0	95.6	MEG_3448	Drugs:Aminoglycosides:Aminoglycoside_efflux_pumps:KDPE	NA
contig00031	27846	28235	MARA	0/0	100.0	100.0	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00031	27397	27831	MARR	0/0	100.0	98.6	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00001	66890	68122	MDFA	0/0	100.0	98.4	MEG_3737	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDFA	NA
contig00039	19120	20367	MDTA	0/0	100.0	96.5	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00039	15998	19120	MDTB	0/0	100.0	96.9	MEG_3747	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTB	NA
contig00039	12920	15997	MDTC	0/0	100.0	96.7	MEG_3749	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTC	NA
contig00007	189896	191053	MDTE	0/0	100.0	99.0	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00007	191078	194191	MDTF	0/0	100.0	98.4	MEG_3752	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTF	NA
contig00004	186815	188041	MDTG	0/0	100.0	98.7	MEG_3753	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig00004	196672	197880	MDTH	0/0	100.0	98.0	MEG_3755	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTH	NA
contig00005	288838	289167	MDTI	0/0	100.0	99.7	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00005	288486	288851	MDTJ	0/0	100.0	98.6	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00005	221485	222857	MDTK	0/0	99.9	97.9	MEG_3759	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:MDTK	NA
contig00003	320318	321550	MDTM	0/0	100.0	100.0	MEG_3761	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTM	NA
contig00023	6589	7620	MDTN	0/0	100.0	97.7	MEG_3763	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN	NA
contig00023	7620	9671	MDTO	0/0	100.0	96.6	MEG_3764	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTO	NA
contig00023	9668	11134	MDTP	0/0	100.0	96.5	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig00002	190013	190487	MPHB	0/0	99.6	96.2	MEG_4033	Drugs:MLS:Macrolide_phosphotransferases:MPHB	NA
contig00004	52279	54027	MSBA	0/0	100.0	98.9	MEG_4061	Drugs:Multi-drug_resistance:Multi-drug_ABC_efflux_pumps:MSBA	NA
contig00035	21833	22165	MVRC	0/0	100.0	91.9	MEG_4103	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MVRC	NA
contig00108	578	1408	OXA	0/0	100.0	100.0	MEG_4980	Drugs:betalactams:Class_D_betalactamases:OXA	NA
contig00001	299932	301833	PBP2	0/0	100.0	98.4	MEG_5400	Drugs:betalactams:Penicillin_binding_protein:PBP2	NA
contig00002	131660	132964	PBP4B	0/0	100.0	95.2	MEG_5409	Drugs:betalactams:Penicillin_binding_protein:PBP4B	NA
contig00037	1872	2840	PMRF	0/0	100.0	97.9	MEG_5801	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF	NA
contig00003	237806	238675	ROBA	0/0	100.0	99.9	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00023	31335	31657	SOXS	0/0	99.7	97.8	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00076	2776	3743	SULI	0/0	100.0	100.0	MEG_6615	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULI	NA
contig00060	6479	7294	SULII	0/0	100.0	100.0	MEG_6617	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULII	NA
contig00090	1009	2214	TETB	0/0	100.0	100.0	MEG_7052	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETB	NA
contig00019	31242	32408	UGD	0/0	100.0	96.9	MEG_7328	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:UGD	NA
contig00013	75473	77116	YOGI	0/0	100.0	97.8	MEG_7842	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:YOGI	NA

ID124

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00070	901	1702	aadA2_1	0/0	97.9	99.9	NC_010870	aadA2	Streptomycin
contig00097	117	920	aph(3’’)-Ib_5	0/0	100.0	100.0	AF321551	aph(3’’)-Ib	Streptomycin
contig00093	247	1122	blaCTX-M-27_1	0/0	100.0	100.0	AY156923	blaCTX-M-27	Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig00052	20339	21214	blaCTX-M-55_1	0/0	100.0	100.0	DQ810789	blaCTX-M-55	Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig00074	5984	6643	catA1_1	0/0	100.0	99.8	V00622	catA1	Chloramphenicol
contig00070	6	503	dfrA12_8	0/0	100.0	100.0	AM040708	dfrA12	Trimethoprim
contig00073	5009	6222	floR_2	0/0	99.9	98.2	AF118107	floR	Chloramphenicol, Florfenicol
contig00005	10013	11245	mdf(A)_1	0/0	100.0	99.9	Y08743	mdf(A)
contig00099	68	998	mph(A)_2	2/10	100.0	98.7	U36578	mph(A)	Erythromycin, Azithromycin, Spiramycin, Telithromycin
contig00070	2180	3046	sul1_5	0/0	100.0	99.9	EU780013	sul1	Sulfamethoxazole
contig00090	551	1776	tet(A)_6	0/0	96.2	99.9	AF534183	tet(A)	Doxycycline, Tetracycline
contig00080	800	2005	tet(B)_2	0/0	100.0	100.0	AF326777	tet(B)	Doxycycline, Tetracycline, Minocycline

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00070	923	1702	aadA2	0/0	100.0	99.9	AF156486:5012-5792	aadA2 is an aminoglycoside nucleotidyltransferase gene encoded by plasmids and integrons in K. pneumoniae Salmonella spp. Corynebacterium glutamicum C. freundii and Aeromonas spp.	aminoglycoside
contig00010	39033	42182	acrB	0/0	100.0	100.0	U00096.3:484403-481253	Protein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug/proton antiporter.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00004	135260	138373	acrD	0/0	100.0	100.0	AP009048.1:2586250-2589364	AcrD is an aminoglycoside efflux pump expressed in E. coli. Its expression can be induced by indole and is regulated by baeRS and cpxAR.	aminoglycoside
contig00031	8641	9798	acrE	0/0	100.0	99.9	U00096:3413863-3415021	AcrE is a membrane fusion protein similar to AcrA.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00031	5525	8629	acrF	0/0	100.0	100.0	U00096:3415032-3418137	AcrF is a inner membrane transporter similar to AcrB.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00031	10197	10859	acrS	0/0	100.0	100.0	U00096:3413465-3412802	AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.	cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00097	117	920	APH(3’’)-Ib	0/0	100.0	99.8	AF313472:15593-16397	APH(3’’)-Ib is an aminoglycoside phosphotransferase encoded by plasmids transposons integrative conjugative elements and chromosomes in Enterobacteriaceae and Pseudomonas spp.	aminoglycoside
contig00006	151173	151994	bacA	0/0	100.0	98.7	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00029	57251	57973	baeR	0/0	100.0	99.3	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00029	55851	57254	baeS	0/0	100.0	98.7	AP009048:2165012-2166416	BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.	aminocoumarin, aminoglycoside
contig00074	5984	6643	catI	0/0	100.0	99.8	V00622:243-903	catI is a chromosome and transposon-encoded variant of the cat gene found in Escherichia coli and Acinetobacter baumannii	phenicol
contig00012	53241	54614	cpxA	0/0	100.0	99.0	BA000007.3:4905062-4903688	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	aminocoumarin, aminoglycoside
contig00007	15387	16019	CRP	0/0	100.0	99.4	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00093	247	1122	CTX-M-27	0/0	100.0	100.0	AY156923:0-876	CTX-M-27 is a beta-lactamase found in Escherichia coli	cephalosporin
contig00052	20339	21214	CTX-M-55	0/0	100.0	100.0	DQ885477:0-876	CTX-M-55 is a beta-lactamase found in the Enterobacteriaceae family	cephalosporin
contig00070	6	503	dfrA12	0/0	100.0	100.0	GU585907.1:22103-21605	dfrA12 is an integron-encoded dihydrofolate reductase found in Vibrio cholerae	diaminopyrimidine
contig00002	58523	59695	emrA	0/0	100.0	100.0	AP009048:2810082-2811255	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	fluoroquinolone
contig00002	59712	61250	emrB	0/0	100.0	100.0	U00096:2812615-2814154	emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin.	fluoroquinolone
contig00009	121400	122455	emrK	0/0	100.0	99.9	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00002	57866	58396	emrR	0/0	100.0	99.8	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00009	119862	121400	emrY	0/0	100.0	99.9	D78168:1591-3130	emrY is a multidrug transport that moves substrates across the inner membrane of the Gram-negative E. coli. It is a homolog of emrB.	tetracycline
contig00045	7071	8714	eptA	0/0	100.0	99.9	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00010	37817	39010	Escherichia_coli_acrA	0/0	100.0	100.0	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00013	65396	66529	Escherichia_coli_ampC	0/0	100.0	97.3	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00004	169772	171076	Escherichia_coli_ampC1_beta-lactamase	0/0	100.0	99.9	FN649414.1:2765050-2766355	An ampC-like beta-lactamase identified from Escherichia coli.	cephalosporin, penam
contig00010	127045	128202	Escherichia_coli_ampH	0/0	100.0	100.0	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig00005	10013	11245	Escherichia_coli_mdfA	0/0	100.0	98.4	JQ394987:0-1233	Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter.	benzalkonium_chloride, rhodamine, tetracycline
contig00009	122978	123592	evgA	0/0	100.0	100.0	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00009	123597	127190	evgS	0/0	100.0	100.0	U00096:2484373-2487967	EvgS is a sensor protein that phosphorylates the regulatory protein EvgA. evgS corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	fluoroquinolone, macrolide, penam, tetracycline
contig00073	5009	6223	floR	0/0	100.0	99.8	AF231986:3307-4522	floR is a plasmid or chromosome-encoded chloramphenicol exporter that is found in Bordetella bronchiseptica Escherichia coli Klebsiella pneumoniae Salmonella enterica subsp. enterica serovar Typhimurium str. DT104 and Vibrio cholerae	phenicol
contig00037	1783	2511	gadW	0/0	100.0	94.7	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig00037	592	1416	gadX	0/0	100.0	100.0	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00027	5350	5763	H-NS	0/0	100.0	99.3	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00011	8068	8745	kdpE	0/0	100.0	100.0	U00096.3:721733-721055	kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding.	aminoglycoside
contig00001	231029	231412	marA	0/0	100.0	100.0	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00029	46991	48238	mdtA	0/0	100.0	97.0	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00029	48238	51360	mdtB	0/0	100.0	96.9	U00096:2155262-2158385	MdtB is a transporter that forms a heteromultimer complex with MdtC to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex.	aminocoumarin
contig00029	51361	54438	mdtC	0/0	100.0	97.7	U00096:2158385-2161463	MdtC is a transporter that forms a heteromultimer complex with MdtB to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex. In the absence of MdtB MdtC can form a homomultimer complex that results in a functioning efflux complex with a narrower drug specificity. mdtC corresponds to 3 loci in Pseudomonas aeruginosa PAO1 (gene name: muxC/muxB) and 3 loci in Pseudomonas aeruginosa LESB58.	aminocoumarin
contig00037	6012	7169	mdtE	0/0	100.0	100.0	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00037	2874	5987	mdtF	0/0	100.0	100.0	U00096:3660413-3663527	MdtF is the multidrug inner membrane transporter for the MdtEF-TolC efflux complex.	fluoroquinolone, macrolide, penam
contig00016	18580	19806	mdtG	0/0	100.0	99.4	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00016	28435	29643	mdtH	0/0	100.0	100.0	U00096:1125326-1124117	Multidrug resistance protein MdtH	fluoroquinolone
contig00043	473	1684	mdtM	0/0	98.3	95.5	U00096.3:4568519-4567286	Multidrug resistance protein MdtM	acridine_dye, fluoroquinolone, lincosamide, nucleoside, phenicol
contig00036	22671	23702	mdtN	0/0	100.0	100.0	AP009048.1:4307588-4306556	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	acridine_dye, nucleoside
contig00036	23702	25753	mdtO	0/0	100.0	100.0	AP009048.1:4306557-4304505	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00036	25750	27216	mdtP	0/0	100.0	100.0	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00099	68	970	mphA	0/0	99.7	100.0	D16251.1:2531-1625	The mphA gene encodes for resistance enzyme MPH(2’)-I which preferentially inactivate 14-membered macrolides (e.g.erythromycin telithromycin roxithromycin) over 16-membered macrolides (e.g.tylosin spiramycin). It phosphorylates macrolides at 2’-OH hydroxyl of desosamine sugar of macrolides in a GTP-dependent manner.	macrolide
contig00004	114098	114574	mphB	0/0	100.0	98.3	AE005174.2:3397370-3397847	The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides.	macrolide
contig00005	92961	94709	msbA	0/0	100.0	100.0	U00096.3:966620-968369	MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability.	nitroimidazole
contig00009	17667	18635	pmrF	0/0	100.0	100.0	U00096:2367070-2368039	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide
contig00070	2207	3046	sul1	0/0	100.0	100.0	JF969163:1053-1893	Sul1 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria. It is linked to other resistance genes of class 1 integrons.	sulfonamide
contig00090	551	1776	tet(A)	0/0	96.2	99.9	AF534183.1:2970-4245	TetA is a tetracycline efflux pump found in many species of Gram-negative bacteria.	tetracycline
contig00080	800	2005	tet(B)	0/0	100.0	99.8	AB089595:0-1206	Tet(B) is a tetracycline efflux protein expressed in many Gram-negative bacteria. It confers resistance to tetracycline doxycycline and minocycline but not tigecycline.	tetracycline
contig00006	127309	128796	tolC	0/0	100.0	99.7	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan
contig00034	42513	44156	yojI	0/0	100.0	100.0	U00096.3:2308615-2306971	YojI mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. YojI is capable of pumping out microcin molecules. The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI.	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00070	923	1702	(AGly)aadA2	0/0	100.0	99.9	X68227:66-945	(AGly)aadA2	NA
contig00097	117	920	(AGly)strA	0/0	100.0	99.9	AB366441:22458-23261	(AGly)strA	NA
contig00004	169772	171076	(Bla)AmpC1_Ecoli	0/0	100.0	99.9	FN649414:2765051-2766355	(Bla)AmpC1_Ecoli	NA
contig00013	65396	66529	(Bla)AmpC2_Ecoli	0/0	100.0	97.3	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00010	127045	128202	(Bla)ampH_Ecoli	0/0	100.0	100.0	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00093	247	1122	(Bla)blaCTX-M-27	0/0	100.0	100.0	AY156923:1-876	(Bla)blaCTX-M-27	NA
contig00052	20339	21214	(Bla)blaCTX-M-55	0/0	100.0	100.0	HM748991:321-1196	(Bla)blaCTX-M-55	NA
contig00011	60155	62056	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100.0	100.0	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA
contig00099	68	970	(MLS)mph(A)	0/0	99.7	100.0	DQ445270:1626-2531	(MLS)mph(A)	NA
contig00074	5984	6643	(Phe)catA1	0/0	100.0	99.8	V00622:244-903	(Phe)catA1	NA
contig00073	5009	6223	(Phe)floR	0/0	100.0	99.8	AKLJ01000508:383-1597	(Phe)floR	NA
contig00070	2207	3046	(Sul)sul1	0/0	100.0	100.0	AF071413:6700-7539	(Sul)sul1	NA
contig00090	551	1776	(Tet)tetA	0/0	96.2	99.9	JX424423:94438-95712	(Tet)tetA	NA
contig00080	800	2005	(Tet)tetB	0/0	100.0	99.7	AB089594:1-1206	(Tet)tetB	NA
contig00070	6	503	(Tmt)dfrA12	0/0	100.0	100.0	Z21672:310-807	(Tmt)dfrA12	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00070	911	1702	aadA2	0/0	100.0	100.0	NG_047343.1	ANT(3’’)-Ia family aminoglycoside nucleotidyltransferase AadA2	STREPTOMYCIN
contig00097	117	944	aph(3’’)-Ib	0/0	100.0	100.0	NG_056002.2	aminoglycoside O-phosphotransferase APH(3’’)-Ib	STREPTOMYCIN
contig00093	247	1122	blaCTX-M-27	0/0	100.0	100.0	NG_048976.1	class A extended-spectrum beta-lactamase CTX-M-27	CEPHALOSPORIN
contig00052	20339	21214	blaCTX-M-55	0/0	100.0	100.0	NG_049006.1	class A extended-spectrum beta-lactamase CTX-M-55	CEPHALOSPORIN
contig00013	65396	66529	blaEC-15	0/0	100.0	98.5	NG_049081.1	class C extended-spectrum beta-lactamase EC-15	CEPHALOSPORIN
contig00074	5984	6643	catA1	0/0	100.0	99.8	NG_047582.1	type A-1 chloramphenicol O-acetyltransferase	CHLORAMPHENICOL
contig00070	6	503	dfrA12	0/0	100.0	100.0	NG_047689.1	trimethoprim-resistant dihydrofolate reductase DfrA12	TRIMETHOPRIM
contig00073	5009	6223	floR	0/0	100.0	99.8	NG_047869.1	chloramphenicol/florfenicol efflux MFS transporter FloR	CHLORAMPHENICOL, FLORFENICOL
contig00099	68	998	mph(A)	2/10	100.0	98.7	NG_047986.1	Mph(A) family macrolide 2’-phosphotransferase	MACROLIDE
contig00070	2207	3046	sul1	0/0	100.0	100.0	NG_048082.1	sulfonamide-resistant dihydropteroate synthase Sul1	SULFONAMIDE
contig00090	626	1776	tet(A)	0/0	95.9	99.9	NG_048153.1	tetracycline efflux MFS transporter Tet(A)	TETRACYCLINE
contig00080	800	2005	tet(B)	0/0	100.0	100.0	NG_048163.1	tetracycline efflux MFS transporter Tet(B)	TETRACYCLINE

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00010	37817	39010	ACRA	0/0	100.0	100.0	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00010	39033	42182	ACRB	0/0	100.0	100.0	MEG_401	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRB	NA
contig00004	135260	138373	ACRD	0/0	100.0	100.0	MEG_407	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ACRD	NA
contig00031	8641	9798	ACRE	0/0	100.0	99.9	MEG_408	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRE	NA
contig00031	5525	8629	ACRF	0/0	100.0	100.0	MEG_409	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRF	NA
contig00031	10197	10859	ACRS	0/0	100.0	100.0	MEG_415	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS	NA
contig00010	127045	128202	AMPH	0/0	100.0	100.0	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00070	901	1702	ANT3-DPRIME	0/0	97.9	99.9	MEG_975	Drugs:Aminoglycosides:Aminoglycoside_O-nucleotidyltransferases:ANT3-DPRIME	NA
contig00097	117	944	APH3-DPRIME	0/0	100.0	100.0	MEG_1019	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH3-DPRIME	NA
contig00029	32873	34725	ASMA	0/0	100.0	97.2	MEG_1180	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:ASMA	NA
contig00006	151173	151994	BACA	0/0	100.0	98.9	MEG_1189	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00029	57251	57973	BAER	0/0	100.0	99.3	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00029	55851	57254	BAES	0/0	100.0	98.7	MEG_1193	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES	NA
contig00017	67340	68530	BCR	0/0	100.0	99.9	MEG_1210	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR	NA
contig00013	65396	66529	BLAEC	0/0	100.0	98.5	MEG_1282	Drugs:betalactams:Class_C_betalactamases:BLAEC	NA
contig00074	5984	6643	CATA	0/0	100.0	100.0	MEG_1584	Drugs:Phenicol:Chloramphenicol_acetyltransferases:CATA	NA
contig00012	52546	53244	CPXAR	0/0	100.0	100.0	MEG_2122	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00012	53241	54614	CPXAR	0/0	100.0	100.0	MEG_2121	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00007	15387	16019	CRP	0/0	100.0	99.4	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00062	12915	13857	CTX	0/0	100.0	98.2	MEG_2435	Drugs:betalactams:Class_A_betalactamases:CTX	NA
contig00093	225	1128	CTX	0/0	100.0	99.8	MEG_2401	Drugs:betalactams:Class_A_betalactamases:CTX	NA
contig00070	6	503	DFRA	0/0	100.0	100.0	MEG_2551	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00002	58523	59695	EMRA	0/0	100.0	100.0	MEG_2722	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA	NA
contig00002	59712	61250	EMRB	0/0	100.0	100.0	MEG_2725	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRB	NA
contig00015	14229	15419	EMRD	0/0	100.0	100.0	MEG_2729	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD	NA
contig00009	121400	122563	EMRK	0/0	100.0	99.9	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig00002	57866	58396	EMRR	0/0	100.0	99.8	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00009	119862	121400	EMRY	0/0	100.0	99.9	MEG_2736	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRY	NA
contig00045	7071	8714	EPTA	0/0	100.0	99.9	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig00009	123597	127190	EVGS	0/0	100.0	100.0	MEG_2870	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EVGS	NA
contig00073	5009	6223	FLOR	0/0	100.0	99.8	MEG_2921	Drugs:Phenicol:Phenicol_resistance_MFS_efflux_pumps:FLOR	NA
contig00037	1783	2511	GADW	0/0	100.0	100.0	MEG_3081	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig00037	592	1416	GADX	0/0	100.0	100.0	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00027	5350	5763	HNS	0/0	100.0	99.3	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00011	8068	8745	KDPE	0/0	100.0	100.0	MEG_3448	Drugs:Aminoglycosides:Aminoglycoside_efflux_pumps:KDPE	NA
contig00001	231029	231418	MARA	0/0	100.0	100.0	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00001	231432	231866	MARR	0/0	100.0	100.0	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00005	10013	11245	MDFA	0/0	100.0	100.0	MEG_3737	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDFA	NA
contig00029	46991	48238	MDTA	0/0	100.0	97.0	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00029	48238	51360	MDTB	0/0	100.0	96.9	MEG_3747	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTB	NA
contig00029	51361	54438	MDTC	0/0	100.0	97.7	MEG_3749	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTC	NA
contig00037	6012	7169	MDTE	0/0	100.0	100.0	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00037	2874	5987	MDTF	0/0	100.0	100.0	MEG_3752	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTF	NA
contig00016	18580	19806	MDTG	0/0	100.0	100.0	MEG_3753	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig00016	28435	29643	MDTH	0/0	100.0	100.0	MEG_3755	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTH	NA
contig00001	198307	198636	MDTI	0/0	100.0	100.0	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00001	197955	198320	MDTJ	0/0	100.0	99.5	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00001	126553	127926	MDTK	0/0	100.0	100.0	MEG_3759	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:MDTK	NA
contig00043	473	1684	MDTM	0/0	98.3	95.5	MEG_3761	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTM	NA
contig00036	22671	23702	MDTN	0/0	100.0	100.0	MEG_3763	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN	NA
contig00036	23702	25753	MDTO	0/0	100.0	100.0	MEG_3764	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTO	NA
contig00036	25750	27216	MDTP	0/0	100.0	100.0	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig00099	68	998	MPHA	2/10	100.0	98.7	MEG_4030	Drugs:MLS:Macrolide_phosphotransferases:MPHA	NA
contig00004	114098	114574	MPHB	0/0	100.0	98.3	MEG_4033	Drugs:MLS:Macrolide_phosphotransferases:MPHB	NA
contig00005	92961	94709	MSBA	0/0	100.0	100.0	MEG_4061	Drugs:Multi-drug_resistance:Multi-drug_ABC_efflux_pumps:MSBA	NA
contig00011	60155	62056	PBP2	0/0	100.0	100.0	MEG_5400	Drugs:betalactams:Penicillin_binding_protein:PBP2	NA
contig00004	169772	171076	PBP4B	0/0	100.0	99.9	MEG_5409	Drugs:betalactams:Penicillin_binding_protein:PBP4B	NA
contig00009	17667	18635	PMRF	0/0	100.0	100.0	MEG_5801	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF	NA
contig00035	4214	5083	ROBA	0/0	100.0	99.0	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00053	5785	6108	SOXS	0/0	100.0	100.0	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00070	2206	3173	SULI	0/0	100.0	100.0	MEG_6615	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULI	NA
contig00090	551	1776	TETA	0/0	96.2	99.9	MEG_7024	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETA	NA
contig00080	800	2005	TETB	0/0	100.0	100.0	MEG_7052	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETB	NA
contig00080	2799	3215	TETD	0/0	100.0	100.0	MEG_7070	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETD	NA
contig00034	42513	44156	YOGI	0/0	100.0	100.0	MEG_7842	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:YOGI	NA

ID127

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00057	901	1702	aadA2_1	0/0	97.9	99.9	NC_010870	aadA2	Streptomycin
contig00061	2251	3054	aph(3’’)-Ib_5	0/0	100.0	100.0	AF321551	aph(3’’)-Ib	Streptomycin
contig00061	1415	2251	aph(6)-Id_1	0/0	100.0	99.9	M28829	aph(6)-Id	Streptomycin
contig00010	60490	61365	blaCTX-M-15_1	0/0	100.0	100.0	AY044436	blaCTX-M-15	Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig00082	127	987	blaTEM-1B_1	0/0	100.0	100.0	AY458016	blaTEM-1B	Amoxicillin, Ampicillin, Cephalothin, Piperacillin, Ticarcillin
contig00056	6568	7227	catA1_1	0/0	100.0	99.8	V00622	catA1	Chloramphenicol
contig00057	6	503	dfrA12_8	0/0	100.0	100.0	AM040708	dfrA12	Trimethoprim
contig00085	42	551	dfrA8_1	0/0	100.0	100.0	U10186	dfrA8	Trimethoprim
contig00005	10013	11245	mdf(A)_1	0/0	100.0	99.9	Y08743	mdf(A)
contig00057	2180	3046	sul1_5	0/0	100.0	99.9	EU780013	sul1	Sulfamethoxazole
contig00061	3115	3930	sul2_2	0/0	100.0	100.0	AY034138	sul2	Sulfamethoxazole
contig00067	800	2005	tet(B)_2	0/0	100.0	100.0	AF326777	tet(B)	Doxycycline, Tetracycline, Minocycline

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00057	923	1702	aadA2	0/0	100.0	99.9	AF156486:5012-5792	aadA2 is an aminoglycoside nucleotidyltransferase gene encoded by plasmids and integrons in K. pneumoniae Salmonella spp. Corynebacterium glutamicum C. freundii and Aeromonas spp.	aminoglycoside
contig00006	39033	42182	acrB	0/0	100.0	100.0	U00096.3:484403-481253	Protein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug/proton antiporter.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00008	71642	74755	acrD	0/0	100.0	100.0	AP009048.1:2586250-2589364	AcrD is an aminoglycoside efflux pump expressed in E. coli. Its expression can be induced by indole and is regulated by baeRS and cpxAR.	aminoglycoside
contig00041	8641	9798	acrE	0/0	100.0	99.9	U00096:3413863-3415021	AcrE is a membrane fusion protein similar to AcrA.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00041	5525	8629	acrF	0/0	100.0	99.9	U00096:3415032-3418137	AcrF is a inner membrane transporter similar to AcrB.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00041	10197	10859	acrS	0/0	100.0	100.0	U00096:3413465-3412802	AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.	cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00061	2251	3054	APH(3’’)-Ib	0/0	100.0	99.8	AF313472:15593-16397	APH(3’’)-Ib is an aminoglycoside phosphotransferase encoded by plasmids transposons integrative conjugative elements and chromosomes in Enterobacteriaceae and Pseudomonas spp.	aminoglycoside
contig00061	1415	2251	APH(6)-Id	0/0	100.0	99.8	AF024602:3155-3992	APH(6)-Id is an aminoglycoside phosphotransferase encoded by plasmids integrative conjugative elements and chromosomal genomic islands in K. pneumoniae Salmonella spp. E. coli Shigella flexneri Providencia alcalifaciens Pseudomonas spp. V. cholerae Edwardsiella tarda Pasteurella multocida and Aeromonas bestiarum	aminoglycoside
contig00025	66950	67771	bacA	0/0	100.0	98.7	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00004	211948	212670	baeR	0/0	100.0	99.5	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00004	210548	211951	baeS	0/0	100.0	99.9	AP009048:2165012-2166416	BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.	aminocoumarin, aminoglycoside
contig00056	6568	7227	catI	0/0	100.0	99.8	V00622:243-903	catI is a chromosome and transposon-encoded variant of the cat gene found in Escherichia coli and Acinetobacter baumannii	phenicol
contig00014	61530	62903	cpxA	0/0	100.0	99.0	BA000007.3:4905062-4903688	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	aminocoumarin, aminoglycoside
contig00043	15936	16568	CRP	0/0	100.0	99.4	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00010	60490	61365	CTX-M-15	0/0	100.0	100.0	AY044436:1435-2311	CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family	cephalosporin
contig00057	6	503	dfrA12	0/0	100.0	100.0	GU585907.1:22103-21605	dfrA12 is an integron-encoded dihydrofolate reductase found in Vibrio cholerae	diaminopyrimidine
contig00085	42	551	dfrA8	0/0	100.0	100.0	KJ174469:710-1220	dfrA8 is a transposon-encoded dihydrofolate reductase found in Salmonella enterica	diaminopyrimidine
contig00003	58458	59630	emrA	0/0	100.0	100.0	AP009048:2810082-2811255	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	fluoroquinolone
contig00003	59647	61185	emrB	0/0	100.0	100.0	U00096:2812615-2814154	emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin.	fluoroquinolone
contig00013	121400	122455	emrK	0/0	100.0	99.9	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00003	57801	58331	emrR	0/0	100.0	99.8	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00013	119862	121400	emrY	0/0	100.0	99.9	D78168:1591-3130	emrY is a multidrug transport that moves substrates across the inner membrane of the Gram-negative E. coli. It is a homolog of emrB.	tetracycline
contig00010	128577	130220	eptA	0/0	100.0	99.9	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00006	37817	39010	Escherichia_coli_acrA	0/0	100.0	100.0	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00010	33322	34455	Escherichia_coli_ampC	0/0	100.0	97.3	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00008	106154	107458	Escherichia_coli_ampC1_beta-lactamase	0/0	100.0	99.9	FN649414.1:2765050-2766355	An ampC-like beta-lactamase identified from Escherichia coli.	cephalosporin, penam
contig00006	127045	128202	Escherichia_coli_ampH	0/0	100.0	100.0	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig00005	10013	11245	Escherichia_coli_mdfA	0/0	100.0	98.4	JQ394987:0-1233	Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter.	benzalkonium_chloride, rhodamine, tetracycline
contig00013	122978	123592	evgA	0/0	100.0	100.0	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00013	123597	127190	evgS	0/0	100.0	100.0	U00096:2484373-2487967	EvgS is a sensor protein that phosphorylates the regulatory protein EvgA. evgS corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	fluoroquinolone, macrolide, penam, tetracycline
contig00034	1783	2511	gadW	0/0	100.0	94.7	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig00034	592	1416	gadX	0/0	100.0	100.0	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00011	62969	63382	H-NS	0/0	100.0	99.3	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00016	8068	8745	kdpE	0/0	100.0	100.0	U00096.3:721733-721055	kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding.	aminoglycoside
contig00002	231029	231412	marA	0/0	100.0	100.0	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00004	201688	202935	mdtA	0/0	100.0	98.0	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00004	202935	206057	mdtB	0/0	100.0	99.8	U00096:2155262-2158385	MdtB is a transporter that forms a heteromultimer complex with MdtC to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex.	aminocoumarin
contig00004	206058	209135	mdtC	0/0	100.0	99.9	U00096:2158385-2161463	MdtC is a transporter that forms a heteromultimer complex with MdtB to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex. In the absence of MdtB MdtC can form a homomultimer complex that results in a functioning efflux complex with a narrower drug specificity. mdtC corresponds to 3 loci in Pseudomonas aeruginosa PAO1 (gene name: muxC/muxB) and 3 loci in Pseudomonas aeruginosa LESB58.	aminocoumarin
contig00034	6012	7169	mdtE	0/0	100.0	100.0	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00034	2874	5987	mdtF	0/0	100.0	100.0	U00096:3660413-3663527	MdtF is the multidrug inner membrane transporter for the MdtEF-TolC efflux complex.	fluoroquinolone, macrolide, penam
contig00018	18580	19806	mdtG	0/0	100.0	99.3	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00018	28435	29643	mdtH	0/0	100.0	100.0	U00096:1125326-1124117	Multidrug resistance protein MdtH	fluoroquinolone
contig00038	473	1684	mdtM	0/0	98.3	95.5	U00096.3:4568519-4567286	Multidrug resistance protein MdtM	acridine_dye, fluoroquinolone, lincosamide, nucleoside, phenicol
contig00030	10907	11938	mdtN	0/0	100.0	100.0	AP009048.1:4307588-4306556	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	acridine_dye, nucleoside
contig00030	11938	13989	mdtO	0/0	100.0	100.0	AP009048.1:4306557-4304505	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00030	13986	15452	mdtP	0/0	100.0	100.0	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00008	50480	50956	mphB	0/0	100.0	98.3	AE005174.2:3397370-3397847	The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides.	macrolide
contig00005	92961	94709	msbA	0/0	100.0	100.0	U00096.3:966620-968369	MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability.	nitroimidazole
contig00013	17667	18635	pmrF	0/0	100.0	100.0	U00096:2367070-2368039	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide
contig00057	2207	3046	sul1	0/0	100.0	100.0	JF969163:1053-1893	Sul1 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria. It is linked to other resistance genes of class 1 integrons.	sulfonamide
contig00061	3115	3930	sul2	0/0	100.0	100.0	AY055428.1:21084-20268	Sul2 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria usually found on small plasmids.	sulfonamide
contig00082	127	987	TEM-1	0/0	100.0	99.9	AL513383:161910-162771	TEM-1 is a broad-spectrum beta-lactamase found in many Gram-negative bacteria. Confers resistance to penicillins and first generation cephalosphorins.	cephalosporin, monobactam, penam, penem
contig00067	800	2005	tet(B)	0/0	100.0	99.8	AB089595:0-1206	Tet(B) is a tetracycline efflux protein expressed in many Gram-negative bacteria. It confers resistance to tetracycline doxycycline and minocycline but not tigecycline.	tetracycline
contig00025	43086	44573	tolC	0/0	100.0	99.7	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan
contig00032	42513	44156	yojI	0/0	100.0	100.0	U00096.3:2308615-2306971	YojI mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. YojI is capable of pumping out microcin molecules. The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI.	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00057	923	1702	(AGly)aadA2	0/0	100	99.9	X68227:66-945	(AGly)aadA2	NA
contig00061	2251	3054	(AGly)strA	0/0	100	99.9	AB366441:22458-23261	(AGly)strA	NA
contig00061	1415	2251	(AGly)strB	0/0	100	99.9	FJ474091:264-1100	(AGly)strB	NA
contig00008	106154	107458	(Bla)AmpC1_Ecoli	0/0	100	99.9	FN649414:2765051-2766355	(Bla)AmpC1_Ecoli	NA
contig00010	33322	34455	(Bla)AmpC2_Ecoli	0/0	100	97.3	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00006	127045	128202	(Bla)ampH_Ecoli	0/0	100	100.0	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00010	60490	61365	(Bla)blaCTX-M-15	0/0	100	100.0	JQ686199:261-1136	(Bla)blaCTX-M-15	NA
contig00082	127	987	(Bla)blaTEM-105	0/0	100	99.9	AF516720:215-1075	(Bla)blaTEM-105	NA
contig00016	60155	62056	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100	100.0	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA
contig00056	6568	7227	(Phe)catA1	0/0	100	99.8	V00622:244-903	(Phe)catA1	NA
contig00057	2207	3046	(Sul)sul1	0/0	100	100.0	AF071413:6700-7539	(Sul)sul1	NA
contig00061	3115	3930	(Sul)sul2	0/0	100	100.0	EU360945:1617-2432	(Sul)sul2	NA
contig00067	800	2005	(Tet)tetB	0/0	100	99.7	AB089594:1-1206	(Tet)tetB	NA
contig00057	6	503	(Tmt)dfrA12	0/0	100	100.0	Z21672:310-807	(Tmt)dfrA12	NA
contig00085	42	551	(Tmt)dfrA8	0/0	100	100.0	U10186:711-1220	(Tmt)dfrA8	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00057	911	1702	aadA2	0/0	100	100.0	NG_047343.1	ANT(3’’)-Ia family aminoglycoside nucleotidyltransferase AadA2	STREPTOMYCIN
contig00061	2251	3078	aph(3’’)-Ib	0/0	100	100.0	NG_056002.2	aminoglycoside O-phosphotransferase APH(3’’)-Ib	STREPTOMYCIN
contig00061	1415	2251	aph(6)-Id	0/0	100	100.0	NG_047466.1	aminoglycoside O-phosphotransferase APH(6)-Id	STREPTOMYCIN
contig00010	60490	61365	blaCTX-M-15	0/0	100	100.0	NG_048935.1	class A extended-spectrum beta-lactamase CTX-M-15	CEPHALOSPORIN
contig00010	33322	34455	blaEC-15	0/0	100	98.5	NG_049081.1	class C extended-spectrum beta-lactamase EC-15	CEPHALOSPORIN
contig00082	127	987	blaTEM-1	0/0	100	100.0	NG_050145.1	class A broad-spectrum beta-lactamase TEM-1	BETA-LACTAM
contig00056	6568	7227	catA1	0/0	100	99.8	NG_047582.1	type A-1 chloramphenicol O-acetyltransferase	CHLORAMPHENICOL
contig00057	6	503	dfrA12	0/0	100	100.0	NG_047689.1	trimethoprim-resistant dihydrofolate reductase DfrA12	TRIMETHOPRIM
contig00085	42	551	dfrA8	0/0	100	100.0	NG_047741.1	trimethoprim-resistant dihydrofolate reductase DfrA8	TRIMETHOPRIM
contig00057	2207	3046	sul1	0/0	100	100.0	NG_048082.1	sulfonamide-resistant dihydropteroate synthase Sul1	SULFONAMIDE
contig00061	3115	3930	sul2	0/0	100	100.0	NG_051852.1	sulfonamide-resistant dihydropteroate synthase Sul2	SULFONAMIDE
contig00067	800	2005	tet(B)	0/0	100	100.0	NG_048163.1	tetracycline efflux MFS transporter Tet(B)	TETRACYCLINE

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00006	37817	39010	ACRA	0/0	100.0	100.0	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00006	39033	42182	ACRB	0/0	100.0	100.0	MEG_401	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRB	NA
contig00008	71642	74755	ACRD	0/0	100.0	100.0	MEG_407	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ACRD	NA
contig00041	8641	9798	ACRE	0/0	100.0	99.9	MEG_408	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRE	NA
contig00041	5525	8629	ACRF	0/0	100.0	99.9	MEG_409	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRF	NA
contig00041	10197	10859	ACRS	0/0	100.0	100.0	MEG_415	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS	NA
contig00006	127045	128202	AMPH	0/0	100.0	100.0	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00057	901	1702	ANT3-DPRIME	0/0	97.9	99.9	MEG_975	Drugs:Aminoglycosides:Aminoglycoside_O-nucleotidyltransferases:ANT3-DPRIME	NA
contig00061	2251	3078	APH3-DPRIME	0/0	100.0	100.0	MEG_1019	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH3-DPRIME	NA
contig00061	1415	2251	APH6	0/0	100.0	100.0	MEG_1084	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH6	NA
contig00004	187571	189423	ASMA	0/0	100.0	97.2	MEG_1180	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:ASMA	NA
contig00025	66950	67771	BACA	0/0	100.0	98.9	MEG_1189	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00004	211948	212670	BAER	0/0	100.0	99.5	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00004	210548	211951	BAES	0/0	100.0	99.9	MEG_1193	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES	NA
contig00019	23378	24568	BCR	0/0	100.0	99.9	MEG_1210	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR	NA
contig00010	33322	34455	BLAEC	0/0	100.0	98.5	MEG_1282	Drugs:betalactams:Class_C_betalactamases:BLAEC	NA
contig00056	6568	7232	CATA	0/0	99.1	100.0	MEG_1593	Drugs:Phenicol:Chloramphenicol_acetyltransferases:CATA	NA
contig00014	60835	61533	CPXAR	0/0	100.0	100.0	MEG_2122	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00014	61530	62903	CPXAR	0/0	100.0	100.0	MEG_2121	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00043	15936	16568	CRP	0/0	100.0	99.4	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00053	12905	13847	CTX	0/0	100.0	98.2	MEG_2435	Drugs:betalactams:Class_A_betalactamases:CTX	NA
contig00057	6	503	DFRA	0/0	100.0	100.0	MEG_2551	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00085	42	551	DFRA	0/0	100.0	100.0	MEG_2553	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00003	58458	59630	EMRA	0/0	100.0	100.0	MEG_2722	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA	NA
contig00003	59647	61185	EMRB	0/0	100.0	100.0	MEG_2725	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRB	NA
contig00007	87250	88440	EMRD	0/0	100.0	100.0	MEG_2729	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD	NA
contig00013	121400	122563	EMRK	0/0	100.0	99.9	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig00003	57801	58331	EMRR	0/0	100.0	99.8	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00013	119862	121400	EMRY	0/0	100.0	99.9	MEG_2736	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRY	NA
contig00010	128577	130220	EPTA	0/0	100.0	99.9	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig00013	123597	127190	EVGS	0/0	100.0	100.0	MEG_2870	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EVGS	NA
contig00034	1783	2511	GADW	0/0	100.0	100.0	MEG_3081	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig00034	592	1416	GADX	0/0	100.0	100.0	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00011	62969	63382	HNS	0/0	100.0	99.3	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00016	8068	8745	KDPE	0/0	100.0	100.0	MEG_3448	Drugs:Aminoglycosides:Aminoglycoside_efflux_pumps:KDPE	NA
contig00002	231029	231418	MARA	0/0	100.0	100.0	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00002	231432	231866	MARR	0/0	100.0	100.0	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00005	10013	11245	MDFA	0/0	100.0	100.0	MEG_3737	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDFA	NA
contig00004	201688	202935	MDTA	0/0	100.0	98.0	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00004	202935	206057	MDTB	0/0	100.0	99.8	MEG_3747	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTB	NA
contig00004	206058	209135	MDTC	0/0	100.0	99.9	MEG_3749	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTC	NA
contig00034	6012	7169	MDTE	0/0	100.0	100.0	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00034	2874	5987	MDTF	0/0	100.0	100.0	MEG_3752	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTF	NA
contig00018	18580	19806	MDTG	0/0	100.0	99.9	MEG_3753	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig00018	28435	29643	MDTH	0/0	100.0	100.0	MEG_3755	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTH	NA
contig00002	198307	198636	MDTI	0/0	100.0	100.0	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00002	197955	198320	MDTJ	0/0	100.0	99.5	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00002	126553	127926	MDTK	0/0	100.0	100.0	MEG_3759	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:MDTK	NA
contig00038	473	1684	MDTM	0/0	98.3	95.5	MEG_3761	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTM	NA
contig00030	10907	11938	MDTN	0/0	100.0	100.0	MEG_3763	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN	NA
contig00030	11938	13989	MDTO	0/0	100.0	100.0	MEG_3764	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTO	NA
contig00030	13986	15452	MDTP	0/0	100.0	100.0	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig00008	50480	50956	MPHB	0/0	100.0	98.3	MEG_4033	Drugs:MLS:Macrolide_phosphotransferases:MPHB	NA
contig00005	92961	94709	MSBA	0/0	100.0	100.0	MEG_4061	Drugs:Multi-drug_resistance:Multi-drug_ABC_efflux_pumps:MSBA	NA
contig00016	60155	62056	PBP2	0/0	100.0	100.0	MEG_5400	Drugs:betalactams:Penicillin_binding_protein:PBP2	NA
contig00008	106154	107458	PBP4B	0/0	100.0	99.9	MEG_5409	Drugs:betalactams:Penicillin_binding_protein:PBP4B	NA
contig00013	17667	18635	PMRF	0/0	100.0	100.0	MEG_5801	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF	NA
contig00001	19983	20852	ROBA	0/0	100.0	99.0	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00030	37069	37392	SOXS	0/0	100.0	100.0	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00057	2206	3173	SULI	0/0	100.0	100.0	MEG_6615	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULI	NA
contig00061	3115	3930	SULII	0/0	100.0	100.0	MEG_6617	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULII	NA
contig00067	800	2005	TETB	0/0	100.0	100.0	MEG_7052	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETB	NA
contig00067	2799	3215	TETD	0/0	100.0	100.0	MEG_7070	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETD	NA
contig00032	42513	44156	YOGI	0/0	100.0	100.0	MEG_7842	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:YOGI	NA

ID128

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00043	2620	3408	aadA5_1	0/0	100.0	100.0	AF137361	aadA5	Streptomycin
contig00019	88219	89094	blaCTX-M-15_1	0/0	100.0	100.0	AY044436	blaCTX-M-15	Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig00043	2016	2489	dfrA17_1	0/0	100.0	100.0	FJ460238	dfrA17	Trimethoprim
contig00002	29927	31159	mdf(A)_1	0/0	100.0	97.8	Y08743	mdf(A)
contig00061	68	989	mph(A)_2	1/1	100.0	99.7	U36578	mph(A)	Erythromycin, Azithromycin, Spiramycin, Telithromycin
contig00043	3928	4794	sul1_5	0/0	100.0	99.8	EU780013	sul1	Sulfamethoxazole
contig00050	1712	2958	tet(A)_6	0/0	97.8	100.0	AF534183	tet(A)	Doxycycline, Tetracycline

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00043	2620	3408	aadA5	0/0	100.0	100.0	AF137361:63-852	aadA5 is an aminoglycoside nucleotidyltransferase gene encoded by plasmids transposons and integrons in E. coli K. pneumoniae Kluyvera georgiana P. aeruginosa and E. cloacae	aminoglycoside
contig00002	410572	413721	acrB	0/0	100.0	98.8	U00096.3:484403-481253	Protein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug/proton antiporter.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00001	127119	130232	acrD	0/0	100.0	98.7	AP009048.1:2586250-2589364	AcrD is an aminoglycoside efflux pump expressed in E. coli. Its expression can be induced by indole and is regulated by baeRS and cpxAR.	aminoglycoside
contig00003	365052	366209	acrE	0/0	100.0	98.8	U00096:3413863-3415021	AcrE is a membrane fusion protein similar to AcrA.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00003	366221	369325	acrF	0/0	100.0	96.6	U00096:3415032-3418137	AcrF is a inner membrane transporter similar to AcrB.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00003	363991	364653	acrS	0/0	100.0	98.3	U00096:3413465-3412802	AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.	cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00003	162521	163340	bacA	0/0	99.8	98.3	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00001	533003	533724	baeR	0/0	99.9	97.1	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00001	533721	535124	baeS	0/0	100.0	90.5	AP009048:2165012-2166416	BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.	aminocoumarin, aminoglycoside
contig00019	66950	68317	cpxA	0/0	99.6	98.5	BA000007.3:4905062-4903688	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	aminocoumarin, aminoglycoside
contig00010	15089	15721	CRP	0/0	100.0	99.2	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00019	88219	89094	CTX-M-15	0/0	100.0	100.0	AY044436:1435-2311	CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family	cephalosporin
contig00043	2016	2489	dfrA17	0/0	100.0	100.0	DQ838665:0-474	dfrA17 is an integron-encoded dihydrofolate reductase found in Escherichia coli	diaminopyrimidine
contig00018	93817	94989	emrA	0/0	100.0	98.0	AP009048:2810082-2811255	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	fluoroquinolone
contig00018	95006	96544	emrB	0/0	100.0	98.4	U00096:2812615-2814154	emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin.	fluoroquinolone
contig00001	222947	224002	emrK	0/0	100.0	97.7	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00018	93160	93690	emrR	0/0	100.0	98.5	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00001	224002	225540	emrY	0/0	100.0	97.7	D78168:1591-3130	emrY is a multidrug transport that moves substrates across the inner membrane of the Gram-negative E. coli. It is a homolog of emrB.	tetracycline
contig00011	146400	148043	eptA	0/0	100.0	91.4	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00002	409356	410549	Escherichia_coli_acrA	0/0	100.0	99.1	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00009	131126	132259	Escherichia_coli_ampC	0/0	100.0	97.8	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00002	498471	499628	Escherichia_coli_ampH	0/0	100.0	97.1	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig00014	28735	29067	Escherichia_coli_emrE	0/0	100.0	92.2	Z11877.1:485-818	Member of the small MDR (multidrug resistance) family of transporters, in Escherichia coli this protein provides resistance against a number of positively charged compounds including ethidium bromide and erythromycin, proton-dependent secondary transporter which exchanges protons for compound translocation	macrolide
contig00002	29927	31159	Escherichia_coli_mdfA	0/0	100.0	96.3	JQ394987:0-1233	Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter.	benzalkonium_chloride, rhodamine, tetracycline
contig00001	221809	222423	evgA	0/0	100.0	99.0	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00001	218211	221804	evgS	0/0	100.0	96.3	U00096:2484373-2487967	EvgS is a sensor protein that phosphorylates the regulatory protein EvgA. evgS corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	fluoroquinolone, macrolide, penam, tetracycline
contig00010	188688	189416	gadW	0/0	100.0	100.0	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig00010	189785	190609	gadX	0/0	100.0	93.9	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00008	129735	130148	H-NS	0/0	100.0	99.3	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00002	185280	185952	kdpE	0/0	99.3	95.5	U00096.3:721733-721055	kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding.	aminoglycoside
contig00005	289457	289840	marA	0/0	100.0	99.0	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00001	542737	543984	mdtA	0/0	100.0	95.6	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00001	539615	542737	mdtB	0/0	100.0	96.2	U00096:2155262-2158385	MdtB is a transporter that forms a heteromultimer complex with MdtC to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex.	aminocoumarin
contig00001	536537	539614	mdtC	0/0	100.0	94.0	U00096:2158385-2161463	MdtC is a transporter that forms a heteromultimer complex with MdtB to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex. In the absence of MdtB MdtC can form a homomultimer complex that results in a functioning efflux complex with a narrower drug specificity. mdtC corresponds to 3 loci in Pseudomonas aeruginosa PAO1 (gene name: muxC/muxB) and 3 loci in Pseudomonas aeruginosa LESB58.	aminocoumarin
contig00010	184030	185187	mdtE	0/0	100.0	98.5	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00010	185212	188325	mdtF	0/0	100.0	97.3	U00096:3660413-3663527	MdtF is the multidrug inner membrane transporter for the MdtEF-TolC efflux complex.	fluoroquinolone, macrolide, penam
contig00006	91920	93146	mdtG	0/0	100.0	98.4	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00006	82083	83291	mdtH	0/0	100.0	98.3	U00096:1125326-1124117	Multidrug resistance protein MdtH	fluoroquinolone
contig00004	306755	307987	mdtM	0/0	100.0	95.0	U00096.3:4568519-4567286	Multidrug resistance protein MdtM	acridine_dye, fluoroquinolone, lincosamide, nucleoside, phenicol
contig00011	116127	117158	mdtN	0/0	100.0	96.2	AP009048.1:4307588-4306556	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	acridine_dye, nucleoside
contig00011	114076	116127	mdtO	0/0	100.0	97.1	AP009048.1:4306557-4304505	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00011	112613	114079	mdtP	0/0	100.0	97.6	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00061	68	973	mphA	0/0	100.0	100.0	D16251.1:2531-1625	The mphA gene encodes for resistance enzyme MPH(2’)-I which preferentially inactivate 14-membered macrolides (e.g.erythromycin telithromycin roxithromycin) over 16-membered macrolides (e.g.tylosin spiramycin). It phosphorylates macrolides at 2’-OH hydroxyl of desosamine sugar of macrolides in a GTP-dependent manner.	macrolide
contig00006	217793	219541	msbA	0/0	100.0	98.1	U00096.3:966620-968369	MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability.	nitroimidazole
contig00001	332580	333548	pmrF	0/0	100.0	97.6	U00096:2367070-2368039	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide
contig00043	3955	4794	sul1	0/0	100.0	99.9	JF969163:1053-1893	Sul1 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria. It is linked to other resistance genes of class 1 integrons.	sulfonamide
contig00050	1712	2958	tet(A)	0/0	97.8	100.0	AF534183.1:2970-4245	TetA is a tetracycline efflux pump found in many species of Gram-negative bacteria.	tetracycline
contig00003	135351	136838	tolC	0/0	100.0	98.2	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan
contig00001	597080	598246	ugd	0/0	100.0	96.0	U00096:2099613-2098446	PmrE is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin	peptide
contig00001	391754	393397	yojI	0/0	100.0	97.4	U00096.3:2308615-2306971	YojI mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. YojI is capable of pumping out microcin molecules. The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI.	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00043	2620	3408	(AGly)aadA5	0/0	100	100.0	AF137361:64-852	(AGly)aadA5	NA
contig00009	131126	132259	(Bla)AmpC2_Ecoli	0/0	100	97.8	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00002	498471	499628	(Bla)ampH_Ecoli	0/0	100	97.1	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00019	88219	89094	(Bla)blaCTX-M-15	0/0	100	100.0	JQ686199:261-1136	(Bla)blaCTX-M-15	NA
contig00002	244498	246399	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100	98.7	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA
contig00061	68	973	(MLS)mph(A)	0/0	100	100.0	DQ445270:1626-2531	(MLS)mph(A)	NA
contig00043	3955	4794	(Sul)sul1	0/0	100	99.9	AF071413:6700-7539	(Sul)sul1	NA
contig00050	1684	2958	(Tet)tetA	0/0	100	100.0	JX424423:94438-95712	(Tet)tetA	NA
contig00050	2989	3639	(Tet)tetR	0/0	100	100.0	HF545434:53576-54226	(Tet)tetR	NA
contig00043	2016	2489	(Tmt)dfrA17	0/0	100	100.0	AB126604:98-571	(Tmt)dfrA17	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00043	2620	3408	aadA5	0/0	100	100.0	NG_047357.1	ANT(3’’)-Ia family aminoglycoside nucleotidyltransferase AadA5	STREPTOMYCIN
contig00019	88219	89094	blaCTX-M-15	0/0	100	100.0	NG_048935.1	class A extended-spectrum beta-lactamase CTX-M-15	CEPHALOSPORIN
contig00009	131126	132259	blaEC-5	0/0	100	99.5	NG_049085.1	cephalosporin-hydrolyzing class C beta-lactamase EC-5	CEPHALOSPORIN
contig00043	2016	2489	dfrA17	0/0	100	99.8	NG_047710.1	trimethoprim-resistant dihydrofolate reductase DfrA17	TRIMETHOPRIM
contig00061	68	989	mph(A)	1/1	100	99.7	NG_047986.1	Mph(A) family macrolide 2’-phosphotransferase	MACROLIDE
contig00043	3955	4794	sul1	0/0	100	99.9	NG_048082.1	sulfonamide-resistant dihydropteroate synthase Sul1	SULFONAMIDE
contig00050	1684	2883	tet(A)	0/0	100	100.0	NG_048154.1	tetracycline efflux MFS transporter Tet(A)	TETRACYCLINE

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00002	409356	410549	ACRA	0/0	100.0	99.1	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00002	410572	413721	ACRB	0/0	100.0	98.8	MEG_401	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRB	NA
contig00001	127119	130232	ACRD	0/0	100.0	98.7	MEG_407	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ACRD	NA
contig00003	365052	366209	ACRE	0/0	100.0	98.8	MEG_408	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRE	NA
contig00003	366221	369325	ACRF	0/0	100.0	96.6	MEG_409	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRF	NA
contig00003	363991	364653	ACRS	0/0	100.0	98.3	MEG_415	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS	NA
contig00002	498471	499628	AMPH	0/0	100.0	97.1	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00043	2620	3408	ANT3-DPRIME	0/0	100.0	100.0	MEG_928	Drugs:Aminoglycosides:Aminoglycoside_O-nucleotidyltransferases:ANT3-DPRIME	NA
contig00001	555644	557496	ASMA	0/0	100.0	97.6	MEG_1180	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:ASMA	NA
contig00003	162521	163340	BACA	0/0	99.8	98.5	MEG_1189	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00001	533003	533724	BAER	0/0	99.9	97.1	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00001	533721	535124	BAES	0/0	100.0	90.5	MEG_1193	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES	NA
contig00001	417030	418220	BCR	0/0	100.0	96.6	MEG_1210	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR	NA
contig00009	131126	132259	BLAEC	0/0	100.0	99.5	MEG_1275	Drugs:betalactams:Class_C_betalactamases:BLAEC	NA
contig00019	66255	66953	CPXAR	0/0	100.0	98.1	MEG_2118	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00019	66950	68317	CPXAR	0/0	99.6	99.0	MEG_2121	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00010	15089	15721	CRP	0/0	100.0	99.2	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00043	2016	2489	DFRA	0/0	100.0	100.0	MEG_2547	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00018	93817	94989	EMRA	0/0	100.0	98.0	MEG_2722	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA	NA
contig00018	95006	96544	EMRB	0/0	100.0	98.4	MEG_2725	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRB	NA
contig00007	193341	194531	EMRD	0/0	100.0	97.6	MEG_2729	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD	NA
contig00001	222839	224002	EMRK	0/0	100.0	97.4	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig00018	93160	93690	EMRR	0/0	100.0	98.5	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00001	224002	225540	EMRY	0/0	100.0	97.7	MEG_2736	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRY	NA
contig00011	146400	148043	EPTA	0/0	100.0	91.4	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig00001	218211	221804	EVGS	0/0	100.0	97.4	MEG_2869	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EVGS	NA
contig00010	188688	189416	GADW	0/0	100.0	100.0	MEG_3082	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig00010	189785	190609	GADX	0/0	100.0	93.9	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00008	129735	130148	HNS	0/0	100.0	99.3	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00002	185280	185952	KDPE	0/0	99.3	95.5	MEG_3448	Drugs:Aminoglycosides:Aminoglycoside_efflux_pumps:KDPE	NA
contig00005	289457	289846	MARA	0/0	100.0	99.0	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00005	289861	290295	MARR	0/0	100.0	98.2	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00002	29927	31159	MDFA	0/0	100.0	97.9	MEG_3737	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDFA	NA
contig00001	542737	543984	MDTA	0/0	100.0	95.6	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00001	539615	542737	MDTB	0/0	100.0	96.2	MEG_3747	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTB	NA
contig00001	536537	539614	MDTC	0/0	100.0	94.0	MEG_3749	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTC	NA
contig00010	184030	185187	MDTE	0/0	100.0	98.5	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00010	185212	188325	MDTF	0/0	100.0	97.3	MEG_3752	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTF	NA
contig00006	91920	93146	MDTG	0/0	100.0	98.5	MEG_3753	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig00006	82083	83291	MDTH	0/0	100.0	98.3	MEG_3755	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTH	NA
contig00005	258563	258892	MDTI	0/0	100.0	98.8	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00005	258211	258576	MDTJ	0/0	100.0	98.4	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00005	191249	192621	MDTK	0/0	99.9	97.7	MEG_3759	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:MDTK	NA
contig00004	306755	307987	MDTM	0/0	100.0	95.0	MEG_3761	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTM	NA
contig00011	116127	117158	MDTN	0/0	100.0	96.2	MEG_3763	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN	NA
contig00011	114076	116127	MDTO	0/0	100.0	97.1	MEG_3764	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTO	NA
contig00011	112613	114079	MDTP	0/0	100.0	97.6	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig00061	68	989	MPHA	1/1	100.0	99.7	MEG_4030	Drugs:MLS:Macrolide_phosphotransferases:MPHA	NA
contig00006	217793	219541	MSBA	0/0	100.0	98.1	MEG_4061	Drugs:Multi-drug_resistance:Multi-drug_ABC_efflux_pumps:MSBA	NA
contig00014	28735	29067	MVRC	0/0	100.0	92.2	MEG_4103	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MVRC	NA
contig00002	244498	246399	PBP2	0/0	100.0	98.7	MEG_5400	Drugs:betalactams:Penicillin_binding_protein:PBP2	NA
contig00001	332580	333548	PMRF	0/0	100.0	97.6	MEG_5801	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF	NA
contig00004	247279	248148	ROBA	0/0	100.0	99.0	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00011	84260	84582	SOXS	0/0	99.7	98.1	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00043	3954	4921	SULI	0/0	100.0	99.9	MEG_6615	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULI	NA
contig00050	1684	2958	TETA	0/0	100.0	100.0	MEG_7024	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETA	NA
contig00001	597080	598246	UGD	0/0	100.0	96.0	MEG_7328	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:UGD	NA
contig00001	391754	393397	YOGI	0/0	100.0	97.4	MEG_7842	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:YOGI	NA

ID129E

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00051	1696	2556	aac(3)-IIa_1	0/0	100.0	99.8	X51534	aac(3)-IIa	Gentamicin, Tobramycin
contig00052	1539	2138	aac(6’)-Ib-cr_1	0/0	100.0	100.0	DQ303918	aac(6’)-Ib-cr	Ciprofloxacin
contig00041	8750	9553	aph(3’’)-Ib_5	0/0	100.0	100.0	AF321551	aph(3’’)-Ib	Streptomycin
contig00041	7914	8750	aph(6)-Id_1	0/0	100.0	100.0	M28829	aph(6)-Id	Streptomycin
contig00041	2636	3511	blaCTX-M-15_1	0/0	100.0	100.0	AY044436	blaCTX-M-15	Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig00052	578	1408	blaOXA-1_1	0/0	100.0	100.0	HQ170510	blaOXA-1	Amoxicillin, Amoxicillin+Clavulanic_acid, Ampicillin, Ampicillin+Clavulanic_acid, Cefepime, Piperacillin, Piperacillin+Tazobactam
contig00041	6333	7193	blaTEM-1B_1	0/0	100.0	100.0	AY458016	blaTEM-1B	Amoxicillin, Ampicillin, Cephalothin, Piperacillin, Ticarcillin
contig00042	5401	5883	dfrA14_5	0/0	100.0	99.6	DQ388123	dfrA14	Trimethoprim
contig00010	26021	27253	mdf(A)_1	0/0	100.0	98.4	Y08743	mdf(A)
contig00043	4404	5048	qnrB1_1	0/0	100.0	100.0	DQ351241	qnrB1	Ciprofloxacin
contig00041	9614	10429	sul2_2	0/0	100.0	100.0	AY034138	sul2	Sulfamethoxazole
contig00048	1429	2697	tet(A)_6	1/22	97.8	93.2	AF534183	tet(A)	Doxycycline, Tetracycline

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00051	1696	2556	AAC(3)-IIe	0/0	100.0	99.5	EU022315.1:0-861	AAC(3)-IIe is a plasmid-encoded aminoglycoside acetyltransferase in E. coli	aminoglycoside
contig00052	1539	2138	AAC(6’)-Ib-cr	0/0	100.0	100.0	DQ303918:0-600	AAC(6’)-Ib-cr is an aminoglycoside acetyltransferase encoded by plasmids transposons integrons in Enterobacteriaceae. The aac(6’)-Ib-cr variant gene can induce resistance against aminoglycoside and fluoroquinolone simultaneously	aminoglycoside, fluoroquinolone
contig00011	124628	127777	acrB	0/0	100.0	99.2	U00096.3:484403-481253	Protein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug/proton antiporter.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00004	132897	136010	acrD	0/0	100.0	98.8	AP009048.1:2586250-2589364	AcrD is an aminoglycoside efflux pump expressed in E. coli. Its expression can be induced by indole and is regulated by baeRS and cpxAR.	aminoglycoside
contig00020	102177	103334	acrE	0/0	100.0	99.0	U00096:3413863-3415021	AcrE is a membrane fusion protein similar to AcrA.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00020	103346	106450	acrF	0/0	100.0	98.9	U00096:3415032-3418137	AcrF is a inner membrane transporter similar to AcrB.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00020	101116	101778	acrS	0/0	100.0	99.4	U00096:3413465-3412802	AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.	cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00041	8750	9553	APH(3’’)-Ib	0/0	100.0	99.8	AF313472:15593-16397	APH(3’’)-Ib is an aminoglycoside phosphotransferase encoded by plasmids transposons integrative conjugative elements and chromosomes in Enterobacteriaceae and Pseudomonas spp.	aminoglycoside
contig00041	7914	8750	APH(6)-Id	0/0	100.0	99.9	AF024602:3155-3992	APH(6)-Id is an aminoglycoside phosphotransferase encoded by plasmids integrative conjugative elements and chromosomal genomic islands in K. pneumoniae Salmonella spp. E. coli Shigella flexneri Providencia alcalifaciens Pseudomonas spp. V. cholerae Edwardsiella tarda Pasteurella multocida and Aeromonas bestiarum	aminoglycoside
contig00014	49028	49847	bacA	0/0	99.8	98.7	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00001	287600	288322	baeR	0/0	100.0	97.9	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00001	286200	287603	baeS	0/0	100.0	99.9	AP009048:2165012-2166416	BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.	aminocoumarin, aminoglycoside
contig00028	22469	23842	cpxA	0/0	100.0	98.8	BA000007.3:4905062-4903688	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	aminocoumarin, aminoglycoside
contig00006	15000	15632	CRP	0/0	100.0	99.2	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00041	2636	3511	CTX-M-15	0/0	100.0	100.0	AY044436:1435-2311	CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family	cephalosporin
contig00042	5401	5883	dfrA14	0/0	100.0	99.8	EU780012:2162-2645	dfrA14 is an integron-encoded dihydrofolate reductase found in Escherichia coli	diaminopyrimidine
contig00034	23988	25160	emrA	0/0	100.0	98.3	AP009048:2810082-2811255	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	fluoroquinolone
contig00034	25177	26715	emrB	0/0	100.0	98.4	U00096:2812615-2814154	emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin.	fluoroquinolone
contig00004	40969	42024	emrK	0/0	100.0	99.7	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00034	23331	23861	emrR	0/0	100.0	100.0	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00004	39431	40969	emrY	0/0	100.0	98.2	D78168:1591-3130	emrY is a multidrug transport that moves substrates across the inner membrane of the Gram-negative E. coli. It is a homolog of emrB.	tetracycline
contig00026	18384	20027	eptA	0/0	100.0	99.4	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00011	127800	128993	Escherichia_coli_acrA	0/0	100.0	99.8	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00015	149708	150841	Escherichia_coli_ampC	0/0	100.0	97.7	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00004	100495	101799	Escherichia_coli_ampC1_beta-lactamase	0/0	100.0	98.2	FN649414.1:2765050-2766355	An ampC-like beta-lactamase identified from Escherichia coli.	cephalosporin, penam
contig00011	36338	37495	Escherichia_coli_ampH	0/0	100.0	99.1	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig00013	76660	76992	Escherichia_coli_emrE	0/0	100.0	99.4	Z11877.1:485-818	Member of the small MDR (multidrug resistance) family of transporters, in Escherichia coli this protein provides resistance against a number of positively charged compounds including ethidium bromide and erythromycin, proton-dependent secondary transporter which exchanges protons for compound translocation	macrolide
contig00010	26021	27253	Escherichia_coli_mdfA	0/0	100.0	96.9	JQ394987:0-1233	Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter.	benzalkonium_chloride, rhodamine, tetracycline
contig00004	42548	43162	evgA	0/0	100.0	99.0	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00004	43167	46760	evgS	0/0	100.0	99.5	U00096:2484373-2487967	EvgS is a sensor protein that phosphorylates the regulatory protein EvgA. evgS corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	fluoroquinolone, macrolide, penam, tetracycline
contig00006	191321	192049	gadW	0/0	100.0	94.4	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig00006	192417	193241	gadX	0/0	100.0	97.9	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00003	72256	72669	H-NS	0/0	100.0	99.3	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00007	8002	8674	kdpE	0/0	99.3	97.2	U00096.3:721733-721055	kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding.	aminoglycoside
contig00018	51533	51916	marA	0/0	100.0	99.7	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00001	277340	278587	mdtA	0/0	100.0	98.2	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00001	278587	281709	mdtB	0/0	100.0	97.8	U00096:2155262-2158385	MdtB is a transporter that forms a heteromultimer complex with MdtC to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex.	aminocoumarin
contig00001	281710	284787	mdtC	0/0	100.0	98.2	U00096:2158385-2161463	MdtC is a transporter that forms a heteromultimer complex with MdtB to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex. In the absence of MdtB MdtC can form a homomultimer complex that results in a functioning efflux complex with a narrower drug specificity. mdtC corresponds to 3 loci in Pseudomonas aeruginosa PAO1 (gene name: muxC/muxB) and 3 loci in Pseudomonas aeruginosa LESB58.	aminocoumarin
contig00006	186663	187820	mdtE	0/0	100.0	99.6	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00006	187845	190958	mdtF	0/0	100.0	98.6	U00096:3660413-3663527	MdtF is the multidrug inner membrane transporter for the MdtEF-TolC efflux complex.	fluoroquinolone, macrolide, penam
contig00003	243280	244506	mdtG	0/0	100.0	99.2	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00003	233441	234649	mdtH	0/0	100.0	98.8	U00096:1125326-1124117	Multidrug resistance protein MdtH	fluoroquinolone
contig00022	75713	76945	mdtM	0/0	100.0	95.9	U00096.3:4568519-4567286	Multidrug resistance protein MdtM	acridine_dye, fluoroquinolone, lincosamide, nucleoside, phenicol
contig00016	137105	138136	mdtN	0/0	100.0	97.9	AP009048.1:4307588-4306556	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	acridine_dye, nucleoside
contig00016	135054	137105	mdtO	0/0	100.0	98.3	AP009048.1:4306557-4304505	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00016	133591	135057	mdtP	0/0	100.0	98.2	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00004	157469	157945	mphB	0/0	100.0	97.9	AE005174.2:3397370-3397847	The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides.	macrolide
contig00010	152771	154519	msbA	0/0	100.0	99.0	U00096.3:966620-968369	MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability.	nitroimidazole
contig00052	578	1408	OXA-1	0/0	100.0	100.0	JN420336.1:2230-1399	OXA-1 is a beta-lactamase found in E. coli	cephalosporin, penam
contig00001	476698	477666	pmrF	0/0	100.0	99.4	U00096:2367070-2368039	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide
contig00043	4367	5048	QnrB17	1/1	100.0	99.1	AM919398:0-681	QnrB17 is a plasmid-mediated quinolone resistance protein found in Citrobacter freundii	fluoroquinolone
contig00041	9614	10429	sul2	0/0	100.0	100.0	AY055428.1:21084-20268	Sul2 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria usually found on small plasmids.	sulfonamide
contig00041	6333	7193	TEM-1	0/0	100.0	99.9	AL513383:161910-162771	TEM-1 is a broad-spectrum beta-lactamase found in many Gram-negative bacteria. Confers resistance to penicillins and first generation cephalosphorins.	cephalosporin, monobactam, penam, penem
contig00048	1429	2697	tet(A)	1/22	97.8	93.2	AF534183.1:2970-4245	TetA is a tetracycline efflux pump found in many species of Gram-negative bacteria.	tetracycline
contig00014	25182	26669	tolC	0/0	100.0	98.5	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan
contig00001	223593	224759	ugd	0/0	100.0	96.6	U00096:2099613-2098446	PmrE is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin	peptide
contig00001	427979	429622	yojI	0/0	100.0	98.0	U00096.3:2308615-2306971	YojI mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. YojI is capable of pumping out microcin molecules. The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI.	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00051	1696	2556	(AGly)aac3-IIa	0/0	100.0	99.8	X51534:91-951	(AGly)aac3-IIa	NA
contig00041	8750	9553	(AGly)strA	0/0	100.0	99.9	AB366441:22458-23261	(AGly)strA	NA
contig00041	7914	8750	(AGly)strB	0/0	100.0	100.0	FJ474091:264-1100	(AGly)strB	NA
contig00004	100495	101799	(Bla)AmpC1_Ecoli	0/0	100.0	98.2	FN649414:2765051-2766355	(Bla)AmpC1_Ecoli	NA
contig00015	149708	150841	(Bla)AmpC2_Ecoli	0/0	100.0	97.7	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00011	36338	37495	(Bla)ampH_Ecoli	0/0	100.0	99.1	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00041	2636	3511	(Bla)blaCTX-M-15	0/0	100.0	100.0	JQ686199:261-1136	(Bla)blaCTX-M-15	NA
contig00052	578	1408	(Bla)blaOXA-1	0/0	100.0	100.0	JQ682867:1-831	(Bla)blaOXA-1	NA
contig00041	6333	7193	(Bla)blaTEM-105	0/0	100.0	99.9	AF516720:215-1075	(Bla)blaTEM-105	NA
contig00007	60465	62366	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100.0	99.4	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA
contig00043	4367	5048	(Flq)qnrB1	1/1	100.0	99.8	DQ351241:1-681	(Flq)qnrB1	NA
contig00041	9614	10429	(Sul)sul2	0/0	100.0	100.0	EU360945:1617-2432	(Sul)sul2	NA
contig00048	1429	2725	(Tet)tetA	1/22	100.0	93.3	JX424423:94438-95712	(Tet)tetA	NA
contig00048	757	1398	(Tet)tetR	1/9	98.6	93.1	HF545434:53576-54226	(Tet)tetR	NA
contig00042	5401	5874	(Tmt)dfrA14	0/0	100.0	100.0	GU726917:72-545	(Tmt)dfrA14	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00051	1696	2556	aac(3)-IIe	0/0	100	99.8	NG_047244.1	aminoglycoside N-acetyltransferase AAC(3)-IIe	GENTAMICIN
contig00052	1539	2093	aac(6’)-Ib-D181Y	0/0	100	99.8	NG_067946.1	AAC(6’)-Ib family aminoglycoside 6’-N-acetyltransferase	AMIKACIN, KANAMYCIN, TOBRAMYCIN
contig00041	8750	9577	aph(3’’)-Ib	0/0	100	100.0	NG_056002.2	aminoglycoside O-phosphotransferase APH(3’’)-Ib	STREPTOMYCIN
contig00041	7914	8750	aph(6)-Id	0/0	100	100.0	NG_047464.1	aminoglycoside O-phosphotransferase APH(6)-Id	STREPTOMYCIN
contig00041	2636	3511	blaCTX-M-15	0/0	100	100.0	NG_048935.1	class A extended-spectrum beta-lactamase CTX-M-15	CEPHALOSPORIN
contig00015	149708	150841	blaEC-18	0/0	100	99.2	NG_049083.1	class C extended-spectrum beta-lactamase EC-18	CEPHALOSPORIN
contig00052	578	1408	blaOXA-1	0/0	100	100.0	NG_049392.1	oxacillin-hydrolyzing class D beta-lactamase OXA-1	CEPHALOSPORIN
contig00041	6333	7193	blaTEM-1	0/0	100	100.0	NG_050145.1	class A broad-spectrum beta-lactamase TEM-1	BETA-LACTAM
contig00042	5401	5874	dfrA14	0/0	100	100.0	NG_056035.1	trimethoprim-resistant dihydrofolate reductase DfrA14	TRIMETHOPRIM
contig00043	4404	5048	qnrB1	0/0	100	100.0	NG_050469.1	quinolone resistance pentapeptide repeat protein QnrB1	QUINOLONE
contig00041	9614	10429	sul2	0/0	100	100.0	NG_051852.1	sulfonamide-resistant dihydropteroate synthase Sul2	SULFONAMIDE
contig00048	1526	2725	tet(A)	0/0	100	100.0	NG_048157.1	tetracycline efflux MFS transporter Tet(A)	TETRACYCLINE

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00051	1696	2556	AAC3	0/0	100.0	99.8	MEG_44	Drugs:Aminoglycosides:Aminoglycoside_N-acetyltransferases:AAC3	NA
contig00011	127800	128993	ACRA	0/0	100.0	99.8	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00011	124628	127777	ACRB	0/0	100.0	99.2	MEG_401	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRB	NA
contig00004	132897	136010	ACRD	0/0	100.0	98.8	MEG_407	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ACRD	NA
contig00020	102177	103334	ACRE	0/0	100.0	99.0	MEG_408	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRE	NA
contig00020	103346	106450	ACRF	0/0	100.0	98.9	MEG_409	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRF	NA
contig00020	101116	101778	ACRS	0/0	100.0	99.4	MEG_415	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS	NA
contig00011	36338	37495	AMPH	0/0	100.0	99.1	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00041	8750	9577	APH3-DPRIME	0/0	100.0	100.0	MEG_1019	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH3-DPRIME	NA
contig00041	7914	8750	APH6	0/0	100.0	100.0	MEG_1086	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH6	NA
contig00001	263553	265405	ASMA	0/0	100.0	98.4	MEG_1180	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:ASMA	NA
contig00014	49028	49847	BACA	0/0	99.8	98.9	MEG_1189	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00001	287600	288322	BAER	0/0	100.0	97.9	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00001	286200	287603	BAES	0/0	100.0	99.9	MEG_1193	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES	NA
contig00001	401517	402707	BCR	0/0	100.0	96.7	MEG_1210	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR	NA
contig00015	149708	150841	BLAEC	0/0	100.0	99.2	MEG_1279	Drugs:betalactams:Class_C_betalactamases:BLAEC	NA
contig00028	21774	22472	CPXAR	0/0	100.0	99.9	MEG_2122	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00028	22469	23842	CPXAR	0/0	100.0	99.4	MEG_2121	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00006	15000	15632	CRP	0/0	100.0	99.2	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00005	158191	159133	CTX	0/0	100.0	98.8	MEG_2435	Drugs:betalactams:Class_A_betalactamases:CTX	NA
contig00042	5401	5874	DFRA	0/0	100.0	99.8	MEG_2517	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00034	23988	25160	EMRA	0/0	100.0	98.3	MEG_2722	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA	NA
contig00034	25177	26715	EMRB	0/0	100.0	98.4	MEG_2725	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRB	NA
contig00009	91841	93031	EMRD	0/0	100.0	99.9	MEG_2729	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD	NA
contig00004	40969	42132	EMRK	0/0	100.0	99.7	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig00034	23331	23861	EMRR	0/0	100.0	100.0	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00004	39431	40969	EMRY	0/0	100.0	98.3	MEG_2736	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRY	NA
contig00026	18384	20027	EPTA	0/0	100.0	99.4	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig00004	43167	46760	EVGS	0/0	100.0	99.5	MEG_2870	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EVGS	NA
contig00006	191321	192049	GADW	0/0	100.0	98.6	MEG_3081	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig00006	192417	193241	GADX	0/0	100.0	97.9	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00003	72256	72669	HNS	0/0	100.0	99.3	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00007	8002	8674	KDPE	0/0	99.3	97.2	MEG_3448	Drugs:Aminoglycosides:Aminoglycoside_efflux_pumps:KDPE	NA
contig00018	51527	51916	MARA	0/0	100.0	99.7	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00018	51079	51513	MARR	0/0	100.0	97.5	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00010	26021	27253	MDFA	0/0	100.0	98.5	MEG_3737	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDFA	NA
contig00001	277340	278587	MDTA	0/0	100.0	98.2	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00001	278587	281709	MDTB	0/0	100.0	97.8	MEG_3747	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTB	NA
contig00001	281710	284787	MDTC	0/0	100.0	98.2	MEG_3749	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTC	NA
contig00006	186663	187820	MDTE	0/0	100.0	99.6	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00006	187845	190958	MDTF	0/0	100.0	98.6	MEG_3752	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTF	NA
contig00003	243280	244506	MDTG	0/0	100.0	99.3	MEG_3753	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig00003	233441	234649	MDTH	0/0	100.0	98.8	MEG_3755	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTH	NA
contig00018	90560	90889	MDTI	0/0	100.0	99.4	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00018	90876	91241	MDTJ	0/0	100.0	99.7	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00012	125931	127304	MDTK	0/0	100.0	99.0	MEG_3759	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:MDTK	NA
contig00022	75713	76945	MDTM	0/0	100.0	95.9	MEG_3761	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTM	NA
contig00016	137105	138136	MDTN	0/0	100.0	97.9	MEG_3763	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN	NA
contig00016	135054	137105	MDTO	0/0	100.0	98.3	MEG_3764	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTO	NA
contig00016	133591	135057	MDTP	0/0	100.0	98.2	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig00004	157469	157945	MPHB	0/0	100.0	97.9	MEG_4033	Drugs:MLS:Macrolide_phosphotransferases:MPHB	NA
contig00010	152771	154519	MSBA	0/0	100.0	99.0	MEG_4061	Drugs:Multi-drug_resistance:Multi-drug_ABC_efflux_pumps:MSBA	NA
contig00013	76660	76992	MVRC	0/0	100.0	99.4	MEG_4103	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MVRC	NA
contig00052	578	1408	OXA	0/0	100.0	100.0	MEG_4980	Drugs:betalactams:Class_D_betalactamases:OXA	NA
contig00007	60465	62366	PBP2	0/0	100.0	99.4	MEG_5400	Drugs:betalactams:Penicillin_binding_protein:PBP2	NA
contig00004	100495	101799	PBP4B	0/0	100.0	98.2	MEG_5409	Drugs:betalactams:Penicillin_binding_protein:PBP4B	NA
contig00001	476698	477666	PMRF	0/0	100.0	99.4	MEG_5801	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF	NA
contig00043	4367	5048	QNRB	1/1	100.0	99.1	MEG_5928	Drugs:Fluoroquinolones:Quinolone_resistance_protein_Qnr:QNRB	NA
contig00022	11905	12774	ROBA	0/0	100.0	99.0	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00016	111654	111976	SOXS	0/0	99.7	99.7	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00041	9614	10429	SULII	0/0	100.0	100.0	MEG_6617	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULII	NA
contig00041	5966	7211	TEM	0/0	98.3	99.4	MEG_6875	Drugs:betalactams:Class_A_betalactamases:TEM	NA
contig00048	1526	2725	TETA	0/0	100.0	100.0	MEG_7021	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETA	NA
contig00001	223593	224759	UGD	0/0	100.0	96.6	MEG_7328	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:UGD	NA
contig00001	427979	429622	YOGI	0/0	100.0	98.0	MEG_7842	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:YOGI	NA

ID130

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00028	24441	25244	aph(3’’)-Ib_5	0/0	100.0	100.0	AF321551	aph(3’’)-Ib	Streptomycin
contig00028	23605	24441	aph(6)-Id_1	0/0	100.0	100.0	M28829	aph(6)-Id	Streptomycin
contig00028	16991	17866	blaCTX-M-15_1	0/0	100.0	100.0	AY044436	blaCTX-M-15	Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig00028	22024	22884	blaTEM-1B_1	0/0	100.0	100.0	AY458016	blaTEM-1B	Amoxicillin, Ampicillin, Cephalothin, Piperacillin, Ticarcillin
contig00042	182	664	dfrA14_5	0/0	100.0	99.6	DQ388123	dfrA14	Trimethoprim
contig00003	159075	160307	mdf(A)_1	0/0	100.0	98.9	Y08743	mdf(A)
contig00028	11694	12350	qnrS1_1	0/0	100.0	100.0	AB187515	qnrS1	Ciprofloxacin
contig00028	25305	26120	sul2_2	0/0	100.0	100.0	AY034138	sul2	Sulfamethoxazole
contig00036	1676	2922	tet(A)_6	0/0	97.8	100.0	AF534183	tet(A)	Doxycycline, Tetracycline

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00008	128420	131569	acrB	0/0	100.0	100.0	U00096.3:484403-481253	Protein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug/proton antiporter.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00004	287068	290181	acrD	0/0	100.0	99.7	AP009048.1:2586250-2589364	AcrD is an aminoglycoside efflux pump expressed in E. coli. Its expression can be induced by indole and is regulated by baeRS and cpxAR.	aminoglycoside
contig00027	8778	9935	acrE	0/0	100.0	99.0	U00096:3413863-3415021	AcrE is a membrane fusion protein similar to AcrA.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00027	5662	8766	acrF	0/0	100.0	99.3	U00096:3415032-3418137	AcrF is a inner membrane transporter similar to AcrB.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00027	10334	10996	acrS	0/0	100.0	98.9	U00096:3413465-3412802	AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.	cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00028	24441	25244	APH(3’’)-Ib	0/0	100.0	99.8	AF313472:15593-16397	APH(3’’)-Ib is an aminoglycoside phosphotransferase encoded by plasmids transposons integrative conjugative elements and chromosomes in Enterobacteriaceae and Pseudomonas spp.	aminoglycoside
contig00028	23605	24441	APH(6)-Id	0/0	100.0	99.9	AF024602:3155-3992	APH(6)-Id is an aminoglycoside phosphotransferase encoded by plasmids integrative conjugative elements and chromosomal genomic islands in K. pneumoniae Salmonella spp. E. coli Shigella flexneri Providencia alcalifaciens Pseudomonas spp. V. cholerae Edwardsiella tarda Pasteurella multocida and Aeromonas bestiarum	aminoglycoside
contig00002	339451	340272	bacA	0/0	100.0	99.5	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00001	133846	134568	baeR	0/0	100.0	100.0	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00001	134565	135968	baeS	0/0	100.0	100.0	AP009048:2165012-2166416	BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.	aminocoumarin, aminoglycoside
contig00011	61329	62702	cpxA	0/0	100.0	98.9	BA000007.3:4905062-4903688	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	aminocoumarin, aminoglycoside
contig00009	14930	15562	CRP	0/0	100.0	99.8	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00028	16991	17866	CTX-M-15	0/0	100.0	100.0	AY044436:1435-2311	CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family	cephalosporin
contig00042	182	664	dfrA14	0/0	100.0	99.8	EU780012:2162-2645	dfrA14 is an integron-encoded dihydrofolate reductase found in Escherichia coli	diaminopyrimidine
contig00010	57502	58674	emrA	0/0	100.0	98.2	AP009048:2810082-2811255	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	fluoroquinolone
contig00010	58691	60229	emrB	0/0	100.0	98.2	U00096:2812615-2814154	emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin.	fluoroquinolone
contig00004	180341	181396	emrK	0/0	100.0	99.8	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00010	56845	57375	emrR	0/0	100.0	100.0	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00004	178803	180341	emrY	0/0	100.0	99.0	D78168:1591-3130	emrY is a multidrug transport that moves substrates across the inner membrane of the Gram-negative E. coli. It is a homolog of emrB.	tetracycline
contig00005	178871	180514	eptA	0/0	100.0	100.0	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00008	131592	132785	Escherichia_coli_acrA	0/0	100.0	100.0	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00005	135515	136648	Escherichia_coli_ampC	0/0	100.0	97.3	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00004	244919	246223	Escherichia_coli_ampC1_beta-lactamase	0/0	100.0	100.0	FN649414.1:2765050-2766355	An ampC-like beta-lactamase identified from Escherichia coli.	cephalosporin, penam
contig00008	42298	43455	Escherichia_coli_ampH	0/0	100.0	99.0	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig00003	159075	160307	Escherichia_coli_mdfA	0/0	100.0	97.3	JQ394987:0-1233	Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter.	benzalkonium_chloride, rhodamine, tetracycline
contig00004	181920	182534	evgA	0/0	100.0	100.0	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00004	182539	186132	evgS	0/0	100.0	99.6	U00096:2484373-2487967	EvgS is a sensor protein that phosphorylates the regulatory protein EvgA. evgS corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	fluoroquinolone, macrolide, penam, tetracycline
contig00022	2243	2971	gadW	0/0	100.0	94.7	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig00022	1051	1875	gadX	0/0	100.0	99.6	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00007	121431	121844	H-NS	0/0	100.0	99.5	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00012	7933	8610	kdpE	0/0	100.0	100.0	U00096.3:721733-721055	kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding.	aminoglycoside
contig00001	686055	686438	marA	0/0	100.0	99.7	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00001	143581	144828	mdtA	0/0	100.0	99.5	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00001	140459	143581	mdtB	0/0	100.0	98.7	U00096:2155262-2158385	MdtB is a transporter that forms a heteromultimer complex with MdtC to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex.	aminocoumarin
contig00001	137381	140458	mdtC	0/0	100.0	99.9	U00096:2158385-2161463	MdtC is a transporter that forms a heteromultimer complex with MdtB to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex. In the absence of MdtB MdtC can form a homomultimer complex that results in a functioning efflux complex with a narrower drug specificity. mdtC corresponds to 3 loci in Pseudomonas aeruginosa PAO1 (gene name: muxC/muxB) and 3 loci in Pseudomonas aeruginosa LESB58.	aminocoumarin
contig00022	6472	7629	mdtE	0/0	100.0	100.0	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00022	3334	6447	mdtF	0/0	100.0	100.0	U00096:3660413-3663527	MdtF is the multidrug inner membrane transporter for the MdtEF-TolC efflux complex.	fluoroquinolone, macrolide, penam
contig00003	387886	389112	mdtG	0/0	100.0	99.3	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00003	397743	398951	mdtH	0/0	100.0	97.8	U00096:1125326-1124117	Multidrug resistance protein MdtH	fluoroquinolone
contig00015	70195	71406	mdtM	0/0	98.3	95.9	U00096.3:4568519-4567286	Multidrug resistance protein MdtM	acridine_dye, fluoroquinolone, lincosamide, nucleoside, phenicol
contig00005	210240	211271	mdtN	0/0	100.0	100.0	AP009048.1:4307588-4306556	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	acridine_dye, nucleoside
contig00005	211271	213322	mdtO	0/0	100.0	100.0	AP009048.1:4306557-4304505	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00005	213319	214785	mdtP	0/0	100.0	99.9	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00004	310859	311335	mphB	0/0	100.0	98.3	AE005174.2:3397370-3397847	The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides.	macrolide
contig00003	250991	252739	msbA	0/0	100.0	100.0	U00096.3:966620-968369	MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability.	nitroimidazole
contig00004	62195	63163	pmrF	0/0	100.0	100.0	U00096:2367070-2368039	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide
contig00028	11694	12350	QnrS1	0/0	100.0	100.0	DQ485529.1:0-657	QnrS1 is a plasmid-mediated quinolone resistance protein found in Shigella flexneri	fluoroquinolone
contig00028	25305	26120	sul2	0/0	100.0	100.0	AY055428.1:21084-20268	Sul2 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria usually found on small plasmids.	sulfonamide
contig00028	22024	22884	TEM-1	0/0	100.0	99.9	AL513383:161910-162771	TEM-1 is a broad-spectrum beta-lactamase found in many Gram-negative bacteria. Confers resistance to penicillins and first generation cephalosphorins.	cephalosporin, monobactam, penam, penem
contig00036	1676	2922	tet(A)	0/0	97.8	100.0	AF534183.1:2970-4245	TetA is a tetracycline efflux pump found in many species of Gram-negative bacteria.	tetracycline
contig00002	315586	317073	tolC	0/0	100.0	99.7	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan
contig00004	2068	3711	yojI	0/0	100.0	98.2	U00096.3:2308615-2306971	YojI mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. YojI is capable of pumping out microcin molecules. The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI.	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00028	24441	25244	(AGly)strA	0/0	100	99.9	AB366441:22458-23261	(AGly)strA	NA
contig00028	23605	24441	(AGly)strB	0/0	100	100.0	FJ474091:264-1100	(AGly)strB	NA
contig00004	244919	246223	(Bla)AmpC1_Ecoli	0/0	100	100.0	FN649414:2765051-2766355	(Bla)AmpC1_Ecoli	NA
contig00005	135515	136648	(Bla)AmpC2_Ecoli	0/0	100	97.3	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00008	42298	43455	(Bla)ampH_Ecoli	0/0	100	99.0	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00028	16991	17866	(Bla)blaCTX-M-15	0/0	100	100.0	JQ686199:261-1136	(Bla)blaCTX-M-15	NA
contig00028	22024	22884	(Bla)blaTEM-105	0/0	100	99.9	AF516720:215-1075	(Bla)blaTEM-105	NA
contig00012	60318	62219	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100	99.0	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA
contig00028	11694	12350	(Flq)qnr-S1	0/0	100	100.0	AB187515:9737-10393	(Flq)qnr-S1	NA
contig00028	25305	26120	(Sul)sul2	0/0	100	100.0	EU360945:1617-2432	(Sul)sul2	NA
contig00036	1648	2922	(Tet)tetA	0/0	100	100.0	JX424423:94438-95712	(Tet)tetA	NA
contig00036	2953	3577	(Tet)tetR	0/0	96	100.0	HF545434:53576-54226	(Tet)tetR	NA
contig00042	182	655	(Tmt)dfrA14	0/0	100	100.0	GU726917:72-545	(Tmt)dfrA14	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00028	24441	25268	aph(3’’)-Ib	0/0	100	100.0	NG_056002.2	aminoglycoside O-phosphotransferase APH(3’’)-Ib	STREPTOMYCIN
contig00028	23605	24441	aph(6)-Id	0/0	100	100.0	NG_047464.1	aminoglycoside O-phosphotransferase APH(6)-Id	STREPTOMYCIN
contig00028	16991	17866	blaCTX-M-15	0/0	100	100.0	NG_048935.1	class A extended-spectrum beta-lactamase CTX-M-15	CEPHALOSPORIN
contig00005	135515	136648	blaEC-15	0/0	100	98.6	NG_049081.1	class C extended-spectrum beta-lactamase EC-15	CEPHALOSPORIN
contig00028	22024	22884	blaTEM-1	0/0	100	100.0	NG_050145.1	class A broad-spectrum beta-lactamase TEM-1	BETA-LACTAM
contig00042	182	655	dfrA14	0/0	100	100.0	NG_056035.1	trimethoprim-resistant dihydrofolate reductase DfrA14	TRIMETHOPRIM
contig00028	11694	12350	qnrS1	0/0	100	100.0	NG_050543.1	quinolone resistance pentapeptide repeat protein QnrS1	QUINOLONE
contig00028	25305	26120	sul2	0/0	100	100.0	NG_051852.1	sulfonamide-resistant dihydropteroate synthase Sul2	SULFONAMIDE
contig00036	1648	2847	tet(A)	0/0	100	100.0	NG_048154.1	tetracycline efflux MFS transporter Tet(A)	TETRACYCLINE

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00008	131592	132785	ACRA	0/0	100.0	100.0	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00008	128420	131569	ACRB	0/0	100.0	100.0	MEG_401	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRB	NA
contig00004	287068	290181	ACRD	0/0	100.0	99.7	MEG_407	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ACRD	NA
contig00027	8778	9935	ACRE	0/0	100.0	99.0	MEG_408	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRE	NA
contig00027	5662	8766	ACRF	0/0	100.0	99.3	MEG_409	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRF	NA
contig00027	10334	10996	ACRS	0/0	100.0	98.9	MEG_415	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS	NA
contig00008	42298	43455	AMPH	0/0	100.0	99.0	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00028	24441	25268	APH3-DPRIME	0/0	100.0	100.0	MEG_1019	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH3-DPRIME	NA
contig00028	23605	24441	APH6	0/0	100.0	100.0	MEG_1086	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH6	NA
contig00001	157231	159083	ASMA	0/0	100.0	98.1	MEG_1180	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:ASMA	NA
contig00002	339451	340272	BACA	0/0	100.0	99.5	MEG_1189	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00001	133846	134568	BAER	0/0	100.0	100.0	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00001	134565	135968	BAES	0/0	100.0	100.0	MEG_1193	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES	NA
contig00001	23590	24780	BCR	0/0	100.0	100.0	MEG_1210	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR	NA
contig00005	135515	136648	BLAEC	0/0	100.0	98.6	MEG_1282	Drugs:betalactams:Class_C_betalactamases:BLAEC	NA
contig00011	60634	61332	CPXAR	0/0	100.0	99.9	MEG_2118	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00011	61329	62702	CPXAR	0/0	100.0	99.8	MEG_2121	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00009	14930	15562	CRP	0/0	100.0	99.8	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00042	182	655	DFRA	0/0	100.0	99.8	MEG_2517	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00010	57502	58674	EMRA	0/0	100.0	98.2	MEG_2722	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA	NA
contig00010	58691	60229	EMRB	0/0	100.0	98.2	MEG_2725	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRB	NA
contig00013	25297	26487	EMRD	0/0	100.0	99.9	MEG_2729	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD	NA
contig00004	180341	181504	EMRK	0/0	100.0	99.8	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig00010	56845	57375	EMRR	0/0	100.0	100.0	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00004	178803	180341	EMRY	0/0	100.0	99.0	MEG_2736	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRY	NA
contig00005	178871	180514	EPTA	0/0	100.0	100.0	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig00004	182539	186132	EVGS	0/0	100.0	99.6	MEG_2870	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EVGS	NA
contig00022	2243	2971	GADW	0/0	100.0	100.0	MEG_3081	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig00022	1051	1875	GADX	0/0	100.0	99.6	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00007	121431	121844	HNS	0/0	100.0	99.5	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00012	7933	8610	KDPE	0/0	100.0	100.0	MEG_3448	Drugs:Aminoglycosides:Aminoglycoside_efflux_pumps:KDPE	NA
contig00001	686055	686444	MARA	0/0	100.0	99.7	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00001	686458	686892	MARR	0/0	100.0	97.9	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00003	159075	160307	MDFA	0/0	100.0	99.0	MEG_3737	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDFA	NA
contig00001	143581	144828	MDTA	0/0	100.0	99.5	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00001	140459	143581	MDTB	0/0	100.0	98.7	MEG_3747	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTB	NA
contig00001	137381	140458	MDTC	0/0	100.0	99.9	MEG_3749	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTC	NA
contig00022	6472	7629	MDTE	0/0	100.0	100.0	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00022	3334	6447	MDTF	0/0	100.0	100.0	MEG_3752	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTF	NA
contig00003	387886	389112	MDTG	0/0	100.0	99.9	MEG_3753	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig00003	397743	398951	MDTH	0/0	100.0	97.8	MEG_3755	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTH	NA
contig00001	637619	637948	MDTI	0/0	100.0	99.7	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00001	637267	637632	MDTJ	0/0	100.0	98.9	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00001	565866	567239	MDTK	0/0	100.0	100.0	MEG_3759	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:MDTK	NA
contig00015	70195	71406	MDTM	0/0	98.3	95.9	MEG_3761	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTM	NA
contig00005	210240	211271	MDTN	0/0	100.0	100.0	MEG_3763	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN	NA
contig00005	211271	213322	MDTO	0/0	100.0	100.0	MEG_3764	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTO	NA
contig00005	213319	214785	MDTP	0/0	100.0	99.9	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig00004	310859	311335	MPHB	0/0	100.0	98.3	MEG_4033	Drugs:MLS:Macrolide_phosphotransferases:MPHB	NA
contig00003	250991	252739	MSBA	0/0	100.0	100.0	MEG_4061	Drugs:Multi-drug_resistance:Multi-drug_ABC_efflux_pumps:MSBA	NA
contig00012	60318	62219	PBP2	0/0	100.0	99.0	MEG_5400	Drugs:betalactams:Penicillin_binding_protein:PBP2	NA
contig00004	244919	246223	PBP4B	0/0	100.0	100.0	MEG_5409	Drugs:betalactams:Penicillin_binding_protein:PBP4B	NA
contig00004	62195	63163	PMRF	0/0	100.0	100.0	MEG_5801	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF	NA
contig00028	11694	12350	QNRS	0/0	100.0	100.0	MEG_6020	Drugs:Fluoroquinolones:Quinolone_resistance_protein_Qnr:QNRS	NA
contig00015	21744	22613	ROBA	0/0	100.0	99.0	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00019	18586	18908	SOXS	0/0	99.7	99.4	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00028	25305	26120	SULII	0/0	100.0	100.0	MEG_6617	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULII	NA
contig00028	21657	22902	TEM	0/0	98.3	99.4	MEG_6875	Drugs:betalactams:Class_A_betalactamases:TEM	NA
contig00036	1648	2922	TETA	0/0	100.0	100.0	MEG_7024	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETA	NA
contig00004	2068	3711	YOGI	0/0	100.0	98.2	MEG_7842	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:YOGI	NA

ID134

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00374	1695	2555	aac(3)-IIa_1	0/0	100.0	99.8	X51534	aac(3)-IIa	Gentamicin, Tobramycin
contig00534	1539	2138	aac(6’)-Ib-cr_1	0/0	100.0	100.0	DQ303918	aac(6’)-Ib-cr	Ciprofloxacin
contig00618	1261	2028	aph(3’’)-Ib_5	0/0	95.5	100.0	AF321551	aph(3’’)-Ib	Streptomycin
contig00618	425	1261	aph(6)-Id_1	0/0	100.0	100.0	M28829	aph(6)-Id	Streptomycin
contig00142	560	1435	blaCTX-M-15_1	0/0	100.0	100.0	AY044436	blaCTX-M-15	Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig00534	578	1408	blaOXA-1_1	0/0	100.0	100.0	HQ170510	blaOXA-1	Amoxicillin, Amoxicillin+Clavulanic_acid, Ampicillin, Ampicillin+Clavulanic_acid, Cefepime, Piperacillin, Piperacillin+Tazobactam
contig00354	275	1135	blaTEM-1B_1	0/0	100.0	100.0	AY458016	blaTEM-1B	Amoxicillin, Ampicillin, Cephalothin, Piperacillin, Ticarcillin
contig00057	5401	5883	dfrA14_5	0/0	100.0	99.6	DQ388123	dfrA14	Trimethoprim
contig00468	1	1157	mdf(A)_1	0/0	93.8	98.9	Y08743	mdf(A)
contig00755	1	1157	mdf(A)_1	0/0	93.8	98.3	Y08743	mdf(A)
contig00077	4403	5047	qnrB1_1	0/0	100.0	100.0	DQ351241	qnrB1	Ciprofloxacin
contig00047	5804	6460	qnrS1_1	0/0	100.0	100.0	AB187515	qnrS1	Ciprofloxacin
contig00164	77	892	sul2_2	0/0	100.0	100.0	AY034138	sul2	Sulfamethoxazole
contig00165	1429	2697	tet(A)_6	1/22	97.8	93.2	AF534183	tet(A)	Doxycycline, Tetracycline
contig00424	1047	2293	tet(A)_6	0/0	97.8	99.4	AF534183	tet(A)	Doxycycline, Tetracycline

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00374	1695	2555	AAC(3)-IIe	0/0	100.0	99.5	EU022315.1:0-861	AAC(3)-IIe is a plasmid-encoded aminoglycoside acetyltransferase in E. coli	aminoglycoside
contig00534	1539	2138	AAC(6’)-Ib-cr	0/0	100.0	100.0	DQ303918:0-600	AAC(6’)-Ib-cr is an aminoglycoside acetyltransferase encoded by plasmids transposons integrons in Enterobacteriaceae. The aac(6’)-Ib-cr variant gene can induce resistance against aminoglycoside and fluoroquinolone simultaneously	aminoglycoside, fluoroquinolone
contig00313	368	1525	acrE	0/0	100.0	99.0	U00096:3413863-3415021	AcrE is a membrane fusion protein similar to AcrA.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00313	1924	2586	acrS	0/0	100.0	99.4	U00096:3413465-3412802	AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.	cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig02288	39	701	acrS	0/0	100.0	98.9	U00096:3413465-3412802	AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.	cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00618	1261	2028	APH(3’’)-Ib	0/0	95.5	99.7	AF313472:15593-16397	APH(3’’)-Ib is an aminoglycoside phosphotransferase encoded by plasmids transposons integrative conjugative elements and chromosomes in Enterobacteriaceae and Pseudomonas spp.	aminoglycoside
contig00618	425	1261	APH(6)-Id	0/0	100.0	99.9	AF024602:3155-3992	APH(6)-Id is an aminoglycoside phosphotransferase encoded by plasmids integrative conjugative elements and chromosomal genomic islands in K. pneumoniae Salmonella spp. E. coli Shigella flexneri Providencia alcalifaciens Pseudomonas spp. V. cholerae Edwardsiella tarda Pasteurella multocida and Aeromonas bestiarum	aminoglycoside
contig00627	1008	1730	baeR	0/0	100.0	100.0	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00142	560	1435	CTX-M-15	0/0	100.0	100.0	AY044436:1435-2311	CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family	cephalosporin
contig00057	5401	5883	dfrA14	0/0	100.0	99.8	EU780012:2162-2645	dfrA14 is an integron-encoded dihydrofolate reductase found in Escherichia coli	diaminopyrimidine
contig02207	26	556	emrR	0/0	100.0	100.0	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00041	7748	8080	Escherichia_coli_emrE	0/0	100.0	99.4	Z11877.1:485-818	Member of the small MDR (multidrug resistance) family of transporters, in Escherichia coli this protein provides resistance against a number of positively charged compounds including ethidium bromide and erythromycin, proton-dependent secondary transporter which exchanges protons for compound translocation	macrolide
contig00468	1	1157	Escherichia_coli_mdfA	0/0	93.8	97.3	JQ394987:0-1233	Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter.	benzalkonium_chloride, rhodamine, tetracycline
contig00755	1	1157	Escherichia_coli_mdfA	0/0	93.8	96.8	JQ394987:0-1233	Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter.	benzalkonium_chloride, rhodamine, tetracycline
contig00812	265	1089	gadX	0/0	100.0	100.0	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00891	265	1089	gadX	0/0	100.0	97.9	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00361	462	875	H-NS	0/0	100.0	99.3	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig01593	478	1155	kdpE	0/0	100.0	100.0	U00096.3:721733-721055	kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding.	aminoglycoside
contig00076	2473	5595	mdtB	0/0	100.0	98.0	U00096:2155262-2158385	MdtB is a transporter that forms a heteromultimer complex with MdtC to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex.	aminocoumarin
contig00087	2078	5200	mdtB	0/0	100.0	97.8	U00096:2155262-2158385	MdtB is a transporter that forms a heteromultimer complex with MdtC to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex.	aminocoumarin
contig00445	1	1223	mdtM	0/0	99.2	96.0	U00096.3:4568519-4567286	Multidrug resistance protein MdtM	acridine_dye, fluoroquinolone, lincosamide, nucleoside, phenicol
contig01431	1	1121	mdtM	0/0	90.9	96.1	U00096.3:4568519-4567286	Multidrug resistance protein MdtM	acridine_dye, fluoroquinolone, lincosamide, nucleoside, phenicol
contig00289	757	1788	mdtN	0/0	100.0	97.9	AP009048.1:4307588-4306556	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	acridine_dye, nucleoside
contig00346	548	1579	mdtN	0/0	100.0	100.0	AP009048.1:4307588-4306556	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	acridine_dye, nucleoside
contig00534	578	1408	OXA-1	0/0	100.0	100.0	JN420336.1:2230-1399	OXA-1 is a beta-lactamase found in E. coli	cephalosporin, penam
contig00077	4366	5047	QnrB17	1/1	100.0	99.1	AM919398:0-681	QnrB17 is a plasmid-mediated quinolone resistance protein found in Citrobacter freundii	fluoroquinolone
contig00047	5804	6460	QnrS1	0/0	100.0	100.0	DQ485529.1:0-657	QnrS1 is a plasmid-mediated quinolone resistance protein found in Shigella flexneri	fluoroquinolone
contig00164	77	892	sul2	0/0	100.0	100.0	AY055428.1:21084-20268	Sul2 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria usually found on small plasmids.	sulfonamide
contig00354	275	1135	TEM-1	0/0	100.0	99.9	AL513383:161910-162771	TEM-1 is a broad-spectrum beta-lactamase found in many Gram-negative bacteria. Confers resistance to penicillins and first generation cephalosphorins.	cephalosporin, monobactam, penam, penem
contig00165	1429	2697	tet(A)	1/22	97.8	93.2	AF534183.1:2970-4245	TetA is a tetracycline efflux pump found in many species of Gram-negative bacteria.	tetracycline
contig00424	1047	2293	tet(A)	0/0	97.8	99.4	AF534183.1:2970-4245	TetA is a tetracycline efflux pump found in many species of Gram-negative bacteria.	tetracycline
contig00107	60	1226	ugd	0/0	100.0	96.1	U00096:2099613-2098446	PmrE is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin	peptide
contig00197	60	1226	ugd	0/0	100.0	96.6	U00096:2099613-2098446	PmrE is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin	peptide
contig00547	235	1878	yojI	0/0	100.0	98.2	U00096.3:2308615-2306971	YojI mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. YojI is capable of pumping out microcin molecules. The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI.	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00374	1695	2555	(AGly)aac3-IIa	0/0	100.0	99.8	X51534:91-951	(AGly)aac3-IIa	NA
contig00618	1261	2028	(AGly)strA	0/0	95.5	99.9	AB366441:22458-23261	(AGly)strA	NA
contig00618	425	1261	(AGly)strB	0/0	100.0	100.0	FJ474091:264-1100	(AGly)strB	NA
contig00142	560	1435	(Bla)blaCTX-M-15	0/0	100.0	100.0	JQ686199:261-1136	(Bla)blaCTX-M-15	NA
contig00534	578	1408	(Bla)blaOXA-1	0/0	100.0	100.0	JQ682867:1-831	(Bla)blaOXA-1	NA
contig00354	275	1135	(Bla)blaTEM-105	0/0	100.0	99.9	AF516720:215-1075	(Bla)blaTEM-105	NA
contig00047	5804	6460	(Flq)qnr-S1	0/0	100.0	100.0	AB187515:9737-10393	(Flq)qnr-S1	NA
contig00077	4366	5047	(Flq)qnrB1	1/1	100.0	99.8	DQ351241:1-681	(Flq)qnrB1	NA
contig00164	77	892	(Sul)sul2	0/0	100.0	100.0	EU360945:1617-2432	(Sul)sul2	NA
contig00165	1429	2725	(Tet)tetA	1/22	100.0	93.3	JX424423:94438-95712	(Tet)tetA	NA
contig00424	1019	2293	(Tet)tetA	0/0	100.0	99.4	JX424423:94438-95712	(Tet)tetA	NA
contig00165	757	1398	(Tet)tetR	1/9	98.6	93.1	HF545434:53576-54226	(Tet)tetR	NA
contig00057	5401	5874	(Tmt)dfrA14	0/0	100.0	100.0	GU726917:72-545	(Tmt)dfrA14	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00374	1695	2555	aac(3)-IIe	0/0	100.0	99.8	NG_047244.1	aminoglycoside N-acetyltransferase AAC(3)-IIe	GENTAMICIN
contig00534	1539	2093	aac(6’)-Ib-D181Y	0/0	100.0	99.8	NG_067946.1	AAC(6’)-Ib family aminoglycoside 6’-N-acetyltransferase	AMIKACIN, KANAMYCIN, TOBRAMYCIN
contig00618	1261	2028	aph(3’’)-Ib	0/0	92.8	100.0	NG_056002.2	aminoglycoside O-phosphotransferase APH(3’’)-Ib	STREPTOMYCIN
contig00618	425	1261	aph(6)-Id	0/0	100.0	100.0	NG_047464.1	aminoglycoside O-phosphotransferase APH(6)-Id	STREPTOMYCIN
contig00142	560	1435	blaCTX-M-15	0/0	100.0	100.0	NG_048935.1	class A extended-spectrum beta-lactamase CTX-M-15	CEPHALOSPORIN
contig00534	578	1408	blaOXA-1	0/0	100.0	100.0	NG_049392.1	oxacillin-hydrolyzing class D beta-lactamase OXA-1	CEPHALOSPORIN
contig00354	275	1135	blaTEM-1	0/0	100.0	100.0	NG_050145.1	class A broad-spectrum beta-lactamase TEM-1	BETA-LACTAM
contig00057	5401	5874	dfrA14	0/0	100.0	100.0	NG_056035.1	trimethoprim-resistant dihydrofolate reductase DfrA14	TRIMETHOPRIM
contig00077	4403	5047	qnrB1	0/0	100.0	100.0	NG_050469.1	quinolone resistance pentapeptide repeat protein QnrB1	QUINOLONE
contig00047	5804	6460	qnrS1	0/0	100.0	100.0	NG_050543.1	quinolone resistance pentapeptide repeat protein QnrS1	QUINOLONE
contig00164	77	892	sul2	0/0	100.0	100.0	NG_051852.1	sulfonamide-resistant dihydropteroate synthase Sul2	SULFONAMIDE
contig00165	1526	2725	tet(A)	0/0	100.0	100.0	NG_048157.1	tetracycline efflux MFS transporter Tet(A)	TETRACYCLINE
contig00424	1019	2218	tet(A)	0/0	100.0	100.0	NG_048159.1	tetracycline efflux MFS transporter Tet(A)	TETRACYCLINE

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00374	1695	2555	AAC3	0/0	100.0	99.8	MEG_44	Drugs:Aminoglycosides:Aminoglycoside_N-acetyltransferases:AAC3	NA
contig00313	368	1525	ACRE	0/0	100.0	99.0	MEG_408	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRE	NA
contig00313	1924	2586	ACRS	0/0	100.0	99.4	MEG_415	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS	NA
contig02288	39	701	ACRS	0/0	100.0	98.9	MEG_415	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS	NA
contig00618	1261	2028	APH3-DPRIME	0/0	92.8	100.0	MEG_1019	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH3-DPRIME	NA
contig00618	425	1261	APH6	0/0	100.0	100.0	MEG_1086	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH6	NA
contig00627	1008	1730	BAER	0/0	100.0	100.0	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00341	759	1949	BCR	0/0	100.0	96.7	MEG_1210	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR	NA
contig00785	1	1122	BCR	0/0	94.2	100.0	MEG_1210	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR	NA
contig00001	61926	62868	CTX	0/0	100.0	98.8	MEG_2435	Drugs:betalactams:Class_A_betalactamases:CTX	NA
contig00057	5401	5874	DFRA	0/0	100.0	99.8	MEG_2517	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig01185	122	1312	EMRD	0/0	100.0	100.0	MEG_2729	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD	NA
contig02207	26	556	EMRR	0/0	100.0	100.0	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00812	265	1089	GADX	0/0	100.0	100.0	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00891	265	1089	GADX	0/0	100.0	97.9	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00361	462	875	HNS	0/0	100.0	99.3	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig01593	478	1155	KDPE	0/0	100.0	100.0	MEG_3448	Drugs:Aminoglycosides:Aminoglycoside_efflux_pumps:KDPE	NA
contig01613	588	1022	MARR	0/0	100.0	97.5	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig02692	193	627	MARR	0/0	100.0	100.0	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00468	1	1157	MDFA	0/0	93.8	99.0	MEG_3737	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDFA	NA
contig00755	1	1157	MDFA	0/0	93.8	98.4	MEG_3737	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDFA	NA
contig00076	2473	5595	MDTB	0/0	100.0	98.0	MEG_3747	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTB	NA
contig00087	2078	5200	MDTB	0/0	100.0	97.8	MEG_3747	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTB	NA
contig00445	1	1223	MDTM	0/0	99.2	96.0	MEG_3761	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTM	NA
contig01431	1	1121	MDTM	0/0	90.9	96.1	MEG_3761	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTM	NA
contig00289	757	1788	MDTN	0/0	100.0	97.9	MEG_3763	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN	NA
contig00346	548	1579	MDTN	0/0	100.0	100.0	MEG_3763	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN	NA
contig00041	7748	8080	MVRC	0/0	100.0	99.4	MEG_4103	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MVRC	NA
contig00534	578	1408	OXA	0/0	100.0	100.0	MEG_4980	Drugs:betalactams:Class_D_betalactamases:OXA	NA
contig00077	4366	5047	QNRB	1/1	100.0	99.1	MEG_5928	Drugs:Fluoroquinolones:Quinolone_resistance_protein_Qnr:QNRB	NA
contig00047	5804	6460	QNRS	0/0	100.0	100.0	MEG_6020	Drugs:Fluoroquinolones:Quinolone_resistance_protein_Qnr:QNRS	NA
contig00164	77	892	SULII	0/0	100.0	100.0	MEG_6617	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULII	NA
contig00354	257	1502	TEM	0/0	98.3	99.4	MEG_6875	Drugs:betalactams:Class_A_betalactamases:TEM	NA
contig00165	1526	2725	TETA	0/0	100.0	100.0	MEG_7021	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETA	NA
contig00424	1019	2293	TETA	0/0	100.0	99.4	MEG_7024	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETA	NA
contig00107	60	1226	UGD	0/0	100.0	96.1	MEG_7328	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:UGD	NA
contig00197	60	1226	UGD	0/0	100.0	96.6	MEG_7328	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:UGD	NA
contig00547	235	1878	YOGI	0/0	100.0	98.2	MEG_7842	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:YOGI	NA

ID136

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00053	1409	2212	aph(3’’)-Ib_5	0/0	100.0	100.0	AF321551	aph(3’’)-Ib	Streptomycin
contig00053	573	1409	aph(6)-Id_1	0/0	100.0	100.0	M28829	aph(6)-Id	Streptomycin
contig00046	602	1477	blaCTX-M-15_1	0/0	100.0	100.0	AY044436	blaCTX-M-15	Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig00048	4597	5457	blaTEM-1B_1	0/0	100.0	100.0	AY458016	blaTEM-1B	Amoxicillin, Ampicillin, Cephalothin, Piperacillin, Ticarcillin
contig00074	182	664	dfrA14_5	0/0	100.0	99.6	DQ388123	dfrA14	Trimethoprim
contig00020	64609	65841	mdf(A)_1	0/0	100.0	99.1	Y08743	mdf(A)
contig00048	9559	10480	mph(A)_2	1/1	100.0	99.7	U36578	mph(A)	Erythromycin, Azithromycin, Spiramycin, Telithromycin
contig00046	6118	6774	qnrS1_1	0/0	100.0	100.0	AB187515	qnrS1	Ciprofloxacin
contig00053	2273	3088	sul2_2	0/0	100.0	100.0	AY034138	sul2	Sulfamethoxazole
contig00060	1676	2922	tet(A)_6	0/0	97.8	100.0	AF534183	tet(A)	Doxycycline, Tetracycline

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00010	124682	127831	acrB	0/0	100.0	99.1	U00096.3:484403-481253	Protein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug/proton antiporter.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00012	117709	120822	acrD	0/0	100.0	98.8	AP009048.1:2586250-2589364	AcrD is an aminoglycoside efflux pump expressed in E. coli. Its expression can be induced by indole and is regulated by baeRS and cpxAR.	aminoglycoside
contig00003	270325	271482	acrE	0/0	100.0	98.9	U00096:3413863-3415021	AcrE is a membrane fusion protein similar to AcrA.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00003	271494	274598	acrF	0/0	100.0	99.0	U00096:3415032-3418137	AcrF is a inner membrane transporter similar to AcrB.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00003	269264	269926	acrS	0/0	100.0	98.6	U00096:3413465-3412802	AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.	cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00053	1409	2212	APH(3’’)-Ib	0/0	100.0	99.8	AF313472:15593-16397	APH(3’’)-Ib is an aminoglycoside phosphotransferase encoded by plasmids transposons integrative conjugative elements and chromosomes in Enterobacteriaceae and Pseudomonas spp.	aminoglycoside
contig00053	573	1409	APH(6)-Id	0/0	100.0	99.9	AF024602:3155-3992	APH(6)-Id is an aminoglycoside phosphotransferase encoded by plasmids integrative conjugative elements and chromosomal genomic islands in K. pneumoniae Salmonella spp. E. coli Shigella flexneri Providencia alcalifaciens Pseudomonas spp. V. cholerae Edwardsiella tarda Pasteurella multocida and Aeromonas bestiarum	aminoglycoside
contig00003	60021	60840	bacA	0/0	99.8	98.7	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00002	115493	116215	baeR	0/0	100.0	99.5	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00002	114093	115496	baeS	0/0	100.0	98.7	AP009048:2165012-2166416	BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.	aminocoumarin, aminoglycoside
contig00027	24220	25593	cpxA	0/0	100.0	98.5	BA000007.3:4905062-4903688	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	aminocoumarin, aminoglycoside
contig00006	15000	15632	CRP	0/0	100.0	99.2	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00046	602	1477	CTX-M-15	0/0	100.0	100.0	AY044436:1435-2311	CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family	cephalosporin
contig00074	182	664	dfrA14	0/0	100.0	99.8	EU780012:2162-2645	dfrA14 is an integron-encoded dihydrofolate reductase found in Escherichia coli	diaminopyrimidine
contig00001	54333	55505	emrA	0/0	100.0	98.2	AP009048:2810082-2811255	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	fluoroquinolone
contig00001	55522	57060	emrB	0/0	100.0	98.5	U00096:2812615-2814154	emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin.	fluoroquinolone
contig00012	25955	27010	emrK	0/0	100.0	98.7	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00001	53676	54206	emrR	0/0	100.0	100.0	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00012	24417	25955	emrY	0/0	100.0	98.8	D78168:1591-3130	emrY is a multidrug transport that moves substrates across the inner membrane of the Gram-negative E. coli. It is a homolog of emrB.	tetracycline
contig00024	18431	20074	eptA	0/0	100.0	99.2	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00010	127854	129047	Escherichia_coli_acrA	0/0	100.0	99.8	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00025	50281	51414	Escherichia_coli_ampC	0/0	100.0	97.2	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00012	85287	86591	Escherichia_coli_ampC1_beta-lactamase	0/0	100.0	98.2	FN649414.1:2765050-2766355	An ampC-like beta-lactamase identified from Escherichia coli.	cephalosporin, penam
contig00010	36338	37495	Escherichia_coli_ampH	0/0	100.0	98.7	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig00030	3107	3439	Escherichia_coli_emrE	0/0	100.0	92.5	Z11877.1:485-818	Member of the small MDR (multidrug resistance) family of transporters, in Escherichia coli this protein provides resistance against a number of positively charged compounds including ethidium bromide and erythromycin, proton-dependent secondary transporter which exchanges protons for compound translocation	macrolide
contig00020	64609	65841	Escherichia_coli_mdfA	0/0	100.0	97.6	JQ394987:0-1233	Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter.	benzalkonium_chloride, rhodamine, tetracycline
contig00012	27534	28148	evgA	0/0	100.0	99.0	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00012	28153	31746	evgS	0/0	100.0	99.5	U00096:2484373-2487967	EvgS is a sensor protein that phosphorylates the regulatory protein EvgA. evgS corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	fluoroquinolone, macrolide, penam, tetracycline
contig00006	190046	190774	gadW	0/0	100.0	94.4	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig00006	191142	191966	gadX	0/0	100.0	97.8	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00004	201389	201802	H-NS	0/0	100.0	99.3	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00007	8188	8860	kdpE	0/0	99.3	97.2	U00096.3:721733-721055	kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding.	aminoglycoside
contig00008	119385	119768	marA	0/0	100.0	99.5	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00002	105233	106480	mdtA	0/0	100.0	98.2	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00002	106480	109602	mdtB	0/0	100.0	98.0	U00096:2155262-2158385	MdtB is a transporter that forms a heteromultimer complex with MdtC to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex.	aminocoumarin
contig00002	109603	112680	mdtC	0/0	100.0	98.1	U00096:2158385-2161463	MdtC is a transporter that forms a heteromultimer complex with MdtB to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex. In the absence of MdtB MdtC can form a homomultimer complex that results in a functioning efflux complex with a narrower drug specificity. mdtC corresponds to 3 loci in Pseudomonas aeruginosa PAO1 (gene name: muxC/muxB) and 3 loci in Pseudomonas aeruginosa LESB58.	aminocoumarin
contig00006	185388	186545	mdtE	0/0	100.0	99.7	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00006	186570	189683	mdtF	0/0	100.0	98.6	U00096:3660413-3663527	MdtF is the multidrug inner membrane transporter for the MdtEF-TolC efflux complex.	fluoroquinolone, macrolide, penam
contig00015	96840	98066	mdtG	0/0	100.0	99.2	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00015	87001	88209	mdtH	0/0	100.0	98.8	U00096:1125326-1124117	Multidrug resistance protein MdtH	fluoroquinolone
contig00016	82731	83963	mdtM	0/0	100.0	95.9	U00096.3:4568519-4567286	Multidrug resistance protein MdtM	acridine_dye, fluoroquinolone, lincosamide, nucleoside, phenicol
contig00017	4240	5271	mdtN	0/0	100.0	98.0	AP009048.1:4307588-4306556	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	acridine_dye, nucleoside
contig00017	5271	7322	mdtO	0/0	100.0	98.7	AP009048.1:4306557-4304505	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00017	7319	8785	mdtP	0/0	100.0	98.2	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00048	9575	10480	mphA	0/0	100.0	100.0	D16251.1:2531-1625	The mphA gene encodes for resistance enzyme MPH(2’)-I which preferentially inactivate 14-membered macrolides (e.g.erythromycin telithromycin roxithromycin) over 16-membered macrolides (e.g.tylosin spiramycin). It phosphorylates macrolides at 2’-OH hydroxyl of desosamine sugar of macrolides in a GTP-dependent manner.	macrolide
contig00012	142312	142788	mphB	0/0	100.0	98.3	AE005174.2:3397370-3397847	The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides.	macrolide
contig00011	46198	47946	msbA	0/0	100.0	99.0	U00096.3:966620-968369	MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability.	nitroimidazole
contig00002	304557	305525	pmrF	0/0	100.0	99.4	U00096:2367070-2368039	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide
contig00046	6118	6774	QnrS1	0/0	100.0	100.0	DQ485529.1:0-657	QnrS1 is a plasmid-mediated quinolone resistance protein found in Shigella flexneri	fluoroquinolone
contig00053	2273	3088	sul2	0/0	100.0	100.0	AY055428.1:21084-20268	Sul2 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria usually found on small plasmids.	sulfonamide
contig00048	4597	5457	TEM-1	0/0	100.0	99.9	AL513383:161910-162771	TEM-1 is a broad-spectrum beta-lactamase found in many Gram-negative bacteria. Confers resistance to penicillins and first generation cephalosphorins.	cephalosporin, monobactam, penam, penem
contig00060	1676	2922	tet(A)	0/0	97.8	100.0	AF534183.1:2970-4245	TetA is a tetracycline efflux pump found in many species of Gram-negative bacteria.	tetracycline
contig00003	36175	37662	tolC	0/0	100.0	98.4	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan
contig00002	255895	257538	yojI	0/0	100.0	98.2	U00096.3:2308615-2306971	YojI mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. YojI is capable of pumping out microcin molecules. The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI.	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00053	1409	2212	(AGly)strA	0/0	100	99.9	AB366441:22458-23261	(AGly)strA	NA
contig00053	573	1409	(AGly)strB	0/0	100	100.0	FJ474091:264-1100	(AGly)strB	NA
contig00012	85287	86591	(Bla)AmpC1_Ecoli	0/0	100	98.2	FN649414:2765051-2766355	(Bla)AmpC1_Ecoli	NA
contig00025	50281	51414	(Bla)AmpC2_Ecoli	0/0	100	97.2	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00010	36338	37495	(Bla)ampH_Ecoli	0/0	100	98.7	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00046	602	1477	(Bla)blaCTX-M-15	0/0	100	100.0	JQ686199:261-1136	(Bla)blaCTX-M-15	NA
contig00048	4597	5457	(Bla)blaTEM-105	0/0	100	99.9	AF516720:215-1075	(Bla)blaTEM-105	NA
contig00007	60649	62550	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100	98.7	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA
contig00046	6118	6774	(Flq)qnr-S1	0/0	100	100.0	AB187515:9737-10393	(Flq)qnr-S1	NA
contig00048	9575	10480	(MLS)mph(A)	0/0	100	100.0	DQ445270:1626-2531	(MLS)mph(A)	NA
contig00053	2273	3088	(Sul)sul2	0/0	100	100.0	EU360945:1617-2432	(Sul)sul2	NA
contig00060	1648	2922	(Tet)tetA	0/0	100	100.0	JX424423:94438-95712	(Tet)tetA	NA
contig00074	182	655	(Tmt)dfrA14	0/0	100	100.0	GU726917:72-545	(Tmt)dfrA14	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00053	1409	2236	aph(3’’)-Ib	0/0	100	100.0	NG_056002.2	aminoglycoside O-phosphotransferase APH(3’’)-Ib	STREPTOMYCIN
contig00053	573	1409	aph(6)-Id	0/0	100	100.0	NG_047464.1	aminoglycoside O-phosphotransferase APH(6)-Id	STREPTOMYCIN
contig00046	602	1477	blaCTX-M-15	0/0	100	100.0	NG_048935.1	class A extended-spectrum beta-lactamase CTX-M-15	CEPHALOSPORIN
contig00025	50281	51414	blaEC-13	0/0	100	99.6	NG_049079.1	class C extended-spectrum beta-lactamase EC-13	CEPHALOSPORIN
contig00048	4597	5457	blaTEM-1	0/0	100	100.0	NG_050145.1	class A broad-spectrum beta-lactamase TEM-1	BETA-LACTAM
contig00074	182	655	dfrA14	0/0	100	100.0	NG_056035.1	trimethoprim-resistant dihydrofolate reductase DfrA14	TRIMETHOPRIM
contig00048	9559	10480	mph(A)	1/1	100	99.7	NG_047986.1	Mph(A) family macrolide 2’-phosphotransferase	MACROLIDE
contig00046	6118	6774	qnrS1	0/0	100	100.0	NG_050543.1	quinolone resistance pentapeptide repeat protein QnrS1	QUINOLONE
contig00053	2273	3088	sul2	0/0	100	100.0	NG_051852.1	sulfonamide-resistant dihydropteroate synthase Sul2	SULFONAMIDE
contig00060	1648	2847	tet(A)	0/0	100	100.0	NG_048154.1	tetracycline efflux MFS transporter Tet(A)	TETRACYCLINE

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00010	127854	129047	ACRA	0/0	100.0	99.8	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00010	124682	127831	ACRB	0/0	100.0	99.1	MEG_401	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRB	NA
contig00012	117709	120822	ACRD	0/0	100.0	98.8	MEG_407	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ACRD	NA
contig00003	270325	271482	ACRE	0/0	100.0	98.9	MEG_408	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRE	NA
contig00003	271494	274598	ACRF	0/0	100.0	99.0	MEG_409	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRF	NA
contig00003	269264	269926	ACRS	0/0	100.0	98.6	MEG_415	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS	NA
contig00010	36338	37495	AMPH	0/0	100.0	98.7	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00053	1409	2236	APH3-DPRIME	0/0	100.0	100.0	MEG_1019	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH3-DPRIME	NA
contig00053	573	1409	APH6	0/0	100.0	100.0	MEG_1086	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH6	NA
contig00002	90978	92830	ASMA	0/0	100.0	98.0	MEG_1180	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:ASMA	NA
contig00003	60021	60840	BACA	0/0	99.8	98.9	MEG_1189	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00002	115493	116215	BAER	0/0	100.0	99.5	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00002	114093	115496	BAES	0/0	100.0	98.7	MEG_1193	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES	NA
contig00002	229434	230624	BCR	0/0	100.0	98.2	MEG_1210	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR	NA
contig00025	50281	51414	BLAEC	0/0	100.0	99.6	MEG_1280	Drugs:betalactams:Class_C_betalactamases:BLAEC	NA
contig00027	23525	24223	CPXAR	0/0	100.0	99.4	MEG_2118	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00027	24220	25593	CPXAR	0/0	100.0	99.1	MEG_2121	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00006	15000	15632	CRP	0/0	100.0	99.2	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00074	182	655	DFRA	0/0	100.0	99.8	MEG_2517	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00001	54333	55505	EMRA	0/0	100.0	98.2	MEG_2722	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA	NA
contig00001	55522	57060	EMRB	0/0	100.0	98.5	MEG_2725	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRB	NA
contig00005	111388	112578	EMRD	0/0	100.0	99.9	MEG_2729	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD	NA
contig00012	25955	27118	EMRK	0/0	100.0	98.8	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig00001	53676	54206	EMRR	0/0	100.0	100.0	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00012	24417	25955	EMRY	0/0	100.0	98.9	MEG_2736	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRY	NA
contig00024	18431	20074	EPTA	0/0	100.0	99.2	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig00012	28153	31746	EVGS	0/0	100.0	99.5	MEG_2870	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EVGS	NA
contig00006	190046	190774	GADW	0/0	100.0	98.6	MEG_3081	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig00006	191142	191966	GADX	0/0	100.0	97.8	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00004	201389	201802	HNS	0/0	100.0	99.3	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00007	8188	8860	KDPE	0/0	99.3	97.2	MEG_3448	Drugs:Aminoglycosides:Aminoglycoside_efflux_pumps:KDPE	NA
contig00008	119385	119774	MARA	0/0	100.0	99.5	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00008	119788	120222	MARR	0/0	100.0	97.7	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00020	64609	65841	MDFA	0/0	100.0	99.2	MEG_3737	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDFA	NA
contig00002	105233	106480	MDTA	0/0	100.0	98.2	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00002	106480	109602	MDTB	0/0	100.0	98.0	MEG_3747	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTB	NA
contig00002	109603	112680	MDTC	0/0	100.0	98.1	MEG_3749	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTC	NA
contig00006	185388	186545	MDTE	0/0	100.0	99.7	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00006	186570	189683	MDTF	0/0	100.0	98.6	MEG_3752	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTF	NA
contig00015	96840	98066	MDTG	0/0	100.0	99.3	MEG_3753	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig00015	87001	88209	MDTH	0/0	100.0	98.8	MEG_3755	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTH	NA
contig00008	35375	35704	MDTI	0/0	100.0	99.7	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00008	35023	35388	MDTJ	0/0	100.0	98.9	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00009	134590	135963	MDTK	0/0	100.0	99.0	MEG_3759	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:MDTK	NA
contig00016	82731	83963	MDTM	0/0	100.0	95.9	MEG_3761	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTM	NA
contig00017	4240	5271	MDTN	0/0	100.0	98.0	MEG_3763	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN	NA
contig00017	5271	7322	MDTO	0/0	100.0	98.7	MEG_3764	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTO	NA
contig00017	7319	8785	MDTP	0/0	100.0	98.2	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig00048	9559	10480	MPHA	1/1	100.0	99.7	MEG_4030	Drugs:MLS:Macrolide_phosphotransferases:MPHA	NA
contig00012	142312	142788	MPHB	0/0	100.0	98.3	MEG_4033	Drugs:MLS:Macrolide_phosphotransferases:MPHB	NA
contig00011	46198	47946	MSBA	0/0	100.0	99.0	MEG_4061	Drugs:Multi-drug_resistance:Multi-drug_ABC_efflux_pumps:MSBA	NA
contig00030	3107	3439	MVRC	0/0	100.0	92.5	MEG_4103	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MVRC	NA
contig00007	60649	62550	PBP2	0/0	100.0	98.7	MEG_5400	Drugs:betalactams:Penicillin_binding_protein:PBP2	NA
contig00012	85287	86591	PBP4B	0/0	100.0	98.2	MEG_5409	Drugs:betalactams:Penicillin_binding_protein:PBP4B	NA
contig00002	304557	305525	PMRF	0/0	100.0	99.4	MEG_5801	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF	NA
contig00046	6118	6774	QNRS	0/0	100.0	100.0	MEG_6020	Drugs:Fluoroquinolones:Quinolone_resistance_protein_Qnr:QNRS	NA
contig00016	11978	12847	ROBA	0/0	100.0	99.1	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00017	30402	30725	SOXS	0/0	100.0	100.0	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00053	2273	3088	SULII	0/0	100.0	100.0	MEG_6617	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULII	NA
contig00048	4579	5824	TEM	0/0	98.3	99.4	MEG_6875	Drugs:betalactams:Class_A_betalactamases:TEM	NA
contig00060	1648	2922	TETA	0/0	100.0	100.0	MEG_7024	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETA	NA
contig00002	255895	257538	YOGI	0/0	100.0	98.2	MEG_7842	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:YOGI	NA

ID141

Resfinder

## [1] "No antibiotic resistance genes from Resfinder database were found"

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00006	23	842	bacA	0/0	99.8	98.3	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide

ARG-ANNOT

## [1] "No antibiotic resistance genes from ARG-ANNOT database were found"

NCBI

## [1] "No antibiotic resistance genes from NCBI database were found"

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00006	23	842	BACA	0/0	99.8	98.5	MEG_1189	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA

ID142

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00012	161	949	aadA5_1	0/0	100	100.0	AF137361	aadA5	Streptomycin
contig00999	132	947	aph(3’)-Ia_1	0/0	100	100.0	V00359	aph(3’)-Ia
contig00128	467	1342	blaCTX-M-15_1	0/0	100	99.9	AY044436	blaCTX-M-15	Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig00012	1080	1553	dfrA17_1	0/0	100	100.0	FJ460238	dfrA17	Trimethoprim
contig03009	20	439	fosA_6	0/0	100	94.0	ACZD01000244	fosA	Fosfomycin
contig00163	911	1567	qnrS1_1	0/0	100	100.0	AB187515	qnrS1	Ciprofloxacin
contig00443	268	1134	sul1_5	0/0	100	99.9	EU780013	sul1	Sulfamethoxazole

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00012	161	949	aadA5	0/0	100.0	100.0	AF137361:63-852	aadA5 is an aminoglycoside nucleotidyltransferase gene encoded by plasmids transposons and integrons in E. coli K. pneumoniae Kluyvera georgiana P. aeruginosa and E. cloacae	aminoglycoside
contig00999	134	947	APH(3’)-Ia	0/0	99.8	99.4	BX664015.1:103833-103017	APH(3’)-Ia is a transposon-encoded aminoglycoside phosphotransferase in E. coli and S. enterica. It is identical at the protein sequence to APH(3’)-Ic an aminoglycoside phosphotransferase encoded by plasmids transposons and genomic islands in K. pneumoniae A. baumannii S. marcescens Corynebacterium spp. Photobacterium spp. and Citrobacter spp.	aminoglycoside
contig00128	467	1342	CTX-M-15	0/0	100.0	99.9	AY044436:1435-2311	CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family	cephalosporin
contig00012	1080	1553	dfrA17	0/0	100.0	100.0	DQ838665:0-474	dfrA17 is an integron-encoded dihydrofolate reductase found in Escherichia coli	diaminopyrimidine
contig03009	20	439	FosA5	0/0	100.0	93.3	KP143090.1:1619-1199	fosA5 is a fosfomycin resistance gene isolated from clinical strain of Escherichia coli E265. It is susceptible to amikacin tetracycline and imipenem and resistant to sulphonamide cephalosporins gentamicin ciprofloxacin chloramphenicol and streptomycin	fosfomycin
contig00163	911	1567	QnrS1	0/0	100.0	100.0	DQ485529.1:0-657	QnrS1 is a plasmid-mediated quinolone resistance protein found in Shigella flexneri	fluoroquinolone
contig00443	268	1107	sul1	0/0	100.0	100.0	JF969163:1053-1893	Sul1 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria. It is linked to other resistance genes of class 1 integrons.	sulfonamide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00012	161	949	(AGly)aadA5	0/0	100	100.0	AF137361:64-852	(AGly)aadA5	NA
contig00999	132	947	(AGly)aph3-Ia	0/0	100	99.9	HQ840942:23569-24384	(AGly)aph3-Ia	NA
contig00128	467	1342	(Bla)blaCTX-M-15	0/0	100	99.9	JQ686199:261-1136	(Bla)blaCTX-M-15	NA
contig03009	20	439	(Fcyn)FosA5	0/0	100	93.3	KP143090:1200-1619	(Fcyn)FosA5	NA
contig00163	911	1567	(Flq)qnr-S1	0/0	100	100.0	AB187515:9737-10393	(Flq)qnr-S1	NA
contig00443	268	1107	(Sul)sul1	0/0	100	100.0	AF071413:6700-7539	(Sul)sul1	NA
contig00012	1080	1553	(Tmt)dfrA17	0/0	100	100.0	AB126604:98-571	(Tmt)dfrA17	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00012	161	949	aadA5	0/0	100	100.0	NG_047357.1	ANT(3’’)-Ia family aminoglycoside nucleotidyltransferase AadA5	STREPTOMYCIN
contig00999	132	947	aph(3’)-Ia	0/0	100	100.0	NG_047430.1	aminoglycoside O-phosphotransferase APH(3’)-Ia	KANAMYCIN
contig00128	467	1342	blaCTX-M-143	0/0	100	100.0	NG_067138.1	class A extended-spectrum beta-lactamase CTX-M-143	CEPHALOSPORIN
contig00012	1080	1553	dfrA17	0/0	100	99.8	NG_047710.1	trimethoprim-resistant dihydrofolate reductase DfrA17	TRIMETHOPRIM
contig03009	20	439	fosA_gen	0/0	100	94.0	NG_047881.1	FosA family fosfomycin resistance glutathione transferase	FOSFOMYCIN
contig00163	911	1567	qnrS1	0/0	100	100.0	NG_050543.1	quinolone resistance pentapeptide repeat protein QnrS1	QUINOLONE
contig00443	268	1107	sul1	0/0	100	100.0	NG_048082.1	sulfonamide-resistant dihydropteroate synthase Sul1	SULFONAMIDE

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00012	161	949	ANT3-DPRIME	0/0	100	100.0	MEG_928	Drugs:Aminoglycosides:Aminoglycoside_O-nucleotidyltransferases:ANT3-DPRIME	NA
contig00999	132	947	APH3-PRIME	0/0	100	100.0	MEG_1079	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH3-PRIME	NA
contig00536	681	1365	CPXAR	0/0	98	97.5	MEG_2116	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00012	1080	1553	DFRA	0/0	100	100.0	MEG_2547	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig03009	20	439	FOSA	0/0	100	94.0	MEG_2991	Drugs:Fosfomycin:Fosfomycin_thiol_transferases:FOSA	NA
contig00443	1101	1448	QACEDELTA1	0/0	100	100.0	MEG_5829	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:QACEDELTA1	NA
contig00163	911	1567	QNRS	0/0	100	100.0	MEG_6020	Drugs:Fluoroquinolones:Quinolone_resistance_protein_Qnr:QNRS	NA
contig00443	141	1108	SULI	0/0	100	100.0	MEG_6615	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULI	NA

ID164

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00106	1539	2138	aac(6’)-Ib-cr_1	0/0	100	100.0	DQ303918	aac(6’)-Ib-cr	Ciprofloxacin
contig00091	1773	2561	aadA5_1	0/0	100	100.0	AF137361	aadA5	Streptomycin
contig00087	738	1541	aph(3’’)-Ib_5	0/0	100	100.0	AF321551	aph(3’’)-Ib	Streptomycin
contig00092	1225	2100	blaCTX-M-15_1	0/0	100	100.0	AY044436	blaCTX-M-15	Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig00106	578	1408	blaOXA-1_1	0/0	100	100.0	HQ170510	blaOXA-1	Amoxicillin, Amoxicillin+Clavulanic_acid, Ampicillin, Ampicillin+Clavulanic_acid, Cefepime, Piperacillin, Piperacillin+Tazobactam
contig00087	3920	4780	blaTEM-1B_1	0/0	100	100.0	AY458016	blaTEM-1B	Amoxicillin, Ampicillin, Cephalothin, Piperacillin, Ticarcillin
contig00091	2692	3165	dfrA17_1	0/0	100	100.0	FJ460238	dfrA17	Trimethoprim
contig00001	150954	152186	mdf(A)_1	0/0	100	99.9	Y08743	mdf(A)
contig00091	387	1253	sul1_5	0/0	100	99.9	EU780013	sul1	Sulfamethoxazole
contig00087	1602	2417	sul2_2	0/0	100	100.0	AY034138	sul2	Sulfamethoxazole
contig00096	636	1841	tet(B)_2	0/0	100	99.9	AF326777	tet(B)	Doxycycline, Tetracycline, Minocycline

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00106	1539	2138	AAC(6’)-Ib-cr	0/0	100.0	100.0	DQ303918:0-600	AAC(6’)-Ib-cr is an aminoglycoside acetyltransferase encoded by plasmids transposons integrons in Enterobacteriaceae. The aac(6’)-Ib-cr variant gene can induce resistance against aminoglycoside and fluoroquinolone simultaneously	aminoglycoside, fluoroquinolone
contig00091	1773	2561	aadA5	0/0	100.0	100.0	AF137361:63-852	aadA5 is an aminoglycoside nucleotidyltransferase gene encoded by plasmids transposons and integrons in E. coli K. pneumoniae Kluyvera georgiana P. aeruginosa and E. cloacae	aminoglycoside
contig00008	38756	41905	acrB	0/0	100.0	100.0	U00096.3:484403-481253	Protein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug/proton antiporter.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00006	148083	151196	acrD	0/0	100.0	98.8	AP009048.1:2586250-2589364	AcrD is an aminoglycoside efflux pump expressed in E. coli. Its expression can be induced by indole and is regulated by baeRS and cpxAR.	aminoglycoside
contig00072	5854	8958	acrF	0/0	100.0	100.0	U00096:3415032-3418137	AcrF is a inner membrane transporter similar to AcrB.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00036	601	1263	acrS	0/0	100.0	100.0	U00096:3413465-3412802	AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.	cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00087	738	1541	APH(3’’)-Ib	0/0	100.0	99.8	AF313472:15593-16397	APH(3’’)-Ib is an aminoglycoside phosphotransferase encoded by plasmids transposons integrative conjugative elements and chromosomes in Enterobacteriaceae and Pseudomonas spp.	aminoglycoside
contig00003	70354	71173	bacA	0/0	99.8	98.5	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00023	57249	57971	baeR	0/0	100.0	99.0	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00023	55849	57252	baeS	0/0	100.0	98.7	AP009048:2165012-2166416	BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.	aminocoumarin, aminoglycoside
contig00012	61576	62949	cpxA	0/0	100.0	99.0	BA000007.3:4905062-4903688	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	aminocoumarin, aminoglycoside
contig00009	15081	15713	CRP	0/0	100.0	99.7	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00092	1225	2100	CTX-M-15	0/0	100.0	100.0	AY044436:1435-2311	CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family	cephalosporin
contig00091	2692	3165	dfrA17	0/0	100.0	100.0	DQ838665:0-474	dfrA17 is an integron-encoded dihydrofolate reductase found in Escherichia coli	diaminopyrimidine
contig00010	58703	59875	emrA	0/0	100.0	97.9	AP009048:2810082-2811255	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	fluoroquinolone
contig00010	59892	61430	emrB	0/0	100.0	98.6	U00096:2812615-2814154	emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin.	fluoroquinolone
contig00005	168194	169249	emrK	0/0	100.0	98.0	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00010	58046	58576	emrR	0/0	100.0	99.4	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00005	166656	168194	emrY	0/0	100.0	97.7	D78168:1591-3130	emrY is a multidrug transport that moves substrates across the inner membrane of the Gram-negative E. coli. It is a homolog of emrB.	tetracycline
contig00007	81600	83243	eptA	0/0	100.0	99.9	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00008	37540	38733	Escherichia_coli_acrA	0/0	100.0	100.0	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00007	38239	39372	Escherichia_coli_ampC	0/0	100.0	97.3	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00049	28099	29397	Escherichia_coli_ampC1_beta-lactamase	0/0	99.5	96.1	FN649414.1:2765050-2766355	An ampC-like beta-lactamase identified from Escherichia coli.	cephalosporin, penam
contig00008	126872	128029	Escherichia_coli_ampH	0/0	100.0	100.0	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig00001	150954	152186	Escherichia_coli_mdfA	0/0	100.0	98.4	JQ394987:0-1233	Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter.	benzalkonium_chloride, rhodamine, tetracycline
contig00005	169773	170387	evgA	0/0	100.0	99.2	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00005	170392	173985	evgS	0/0	100.0	96.8	U00096:2484373-2487967	EvgS is a sensor protein that phosphorylates the regulatory protein EvgA. evgS corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	fluoroquinolone, macrolide, penam, tetracycline
contig00042	1784	2512	gadW	0/0	100.0	94.7	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig00042	592	1416	gadX	0/0	100.0	100.0	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00011	41423	41836	H-NS	0/0	100.0	99.3	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00013	8127	8804	kdpE	0/0	100.0	100.0	U00096.3:721733-721055	kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding.	aminoglycoside
contig00004	184592	184975	marA	0/0	100.0	100.0	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00023	46989	48236	mdtA	0/0	100.0	98.1	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00023	48236	51358	mdtB	0/0	100.0	99.9	U00096:2155262-2158385	MdtB is a transporter that forms a heteromultimer complex with MdtC to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex.	aminocoumarin
contig00023	51359	54436	mdtC	0/0	100.0	97.7	U00096:2158385-2161463	MdtC is a transporter that forms a heteromultimer complex with MdtB to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex. In the absence of MdtB MdtC can form a homomultimer complex that results in a functioning efflux complex with a narrower drug specificity. mdtC corresponds to 3 loci in Pseudomonas aeruginosa PAO1 (gene name: muxC/muxB) and 3 loci in Pseudomonas aeruginosa LESB58.	aminocoumarin
contig00042	6013	7170	mdtE	0/0	100.0	100.0	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00042	2875	5988	mdtF	0/0	100.0	100.0	U00096:3660413-3663527	MdtF is the multidrug inner membrane transporter for the MdtEF-TolC efflux complex.	fluoroquinolone, macrolide, penam
contig00034	18580	19806	mdtG	0/0	100.0	99.4	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00034	28435	29643	mdtH	0/0	100.0	99.9	U00096:1125326-1124117	Multidrug resistance protein MdtH	fluoroquinolone
contig00021	70066	71298	mdtM	0/0	100.0	96.3	U00096.3:4568519-4567286	Multidrug resistance protein MdtM	acridine_dye, fluoroquinolone, lincosamide, nucleoside, phenicol
contig00007	112981	114012	mdtN	0/0	100.0	100.0	AP009048.1:4307588-4306556	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	acridine_dye, nucleoside
contig00007	114012	116063	mdtO	0/0	100.0	100.0	AP009048.1:4306557-4304505	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00007	116060	117526	mdtP	0/0	100.0	100.0	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00006	126902	127376	mphB	0/0	99.6	96.2	AE005174.2:3397370-3397847	The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides.	macrolide
contig00001	233901	235649	msbA	0/0	100.0	100.0	U00096.3:966620-968369	MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability.	nitroimidazole
contig00106	578	1408	OXA-1	0/0	100.0	100.0	JN420336.1:2230-1399	OXA-1 is a beta-lactamase found in E. coli	cephalosporin, penam
contig00005	63989	64957	pmrF	0/0	100.0	98.0	U00096:2367070-2368039	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide
contig00091	387	1226	sul1	0/0	100.0	100.0	JF969163:1053-1893	Sul1 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria. It is linked to other resistance genes of class 1 integrons.	sulfonamide
contig00087	1602	2417	sul2	0/0	100.0	100.0	AY055428.1:21084-20268	Sul2 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria usually found on small plasmids.	sulfonamide
contig00087	3920	4780	TEM-1	0/0	100.0	99.9	AL513383:161910-162771	TEM-1 is a broad-spectrum beta-lactamase found in many Gram-negative bacteria. Confers resistance to penicillins and first generation cephalosphorins.	cephalosporin, monobactam, penam, penem
contig00096	636	1841	tet(B)	0/0	100.0	99.7	AB089595:0-1206	Tet(B) is a tetracycline efflux protein expressed in many Gram-negative bacteria. It confers resistance to tetracycline doxycycline and minocycline but not tigecycline.	tetracycline
contig00003	46587	48074	tolC	0/0	100.0	99.9	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan
contig00005	2113	3756	yojI	0/0	100.0	100.0	U00096.3:2308615-2306971	YojI mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. YojI is capable of pumping out microcin molecules. The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI.	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00091	1773	2561	(AGly)aadA5	0/0	100.0	100.0	AF137361:64-852	(AGly)aadA5	NA
contig00087	738	1541	(AGly)strA	0/0	100.0	99.9	AB366441:22458-23261	(AGly)strA	NA
contig00049	28099	29397	(Bla)AmpC1_Ecoli	0/0	99.5	96.1	FN649414:2765051-2766355	(Bla)AmpC1_Ecoli	NA
contig00007	38239	39372	(Bla)AmpC2_Ecoli	0/0	100.0	97.3	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00008	126872	128029	(Bla)ampH_Ecoli	0/0	100.0	100.0	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00092	1225	2100	(Bla)blaCTX-M-15	0/0	100.0	100.0	JQ686199:261-1136	(Bla)blaCTX-M-15	NA
contig00106	578	1408	(Bla)blaOXA-1	0/0	100.0	100.0	JQ682867:1-831	(Bla)blaOXA-1	NA
contig00087	3920	4780	(Bla)blaTEM-105	0/0	100.0	99.9	AF516720:215-1075	(Bla)blaTEM-105	NA
contig00013	60214	62115	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100.0	100.0	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA
contig00091	387	1226	(Sul)sul1	0/0	100.0	100.0	AF071413:6700-7539	(Sul)sul1	NA
contig00087	1602	2417	(Sul)sul2	0/0	100.0	100.0	EU360945:1617-2432	(Sul)sul2	NA
contig00096	636	1841	(Tet)tetB	0/0	100.0	99.6	AB089594:1-1206	(Tet)tetB	NA
contig00091	2692	3165	(Tmt)dfrA17	0/0	100.0	100.0	AB126604:98-571	(Tmt)dfrA17	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00106	1539	2093	aac(6’)-Ib-D181Y	0/0	100	99.8	NG_067946.1	AAC(6’)-Ib family aminoglycoside 6’-N-acetyltransferase	AMIKACIN, KANAMYCIN, TOBRAMYCIN
contig00091	1773	2561	aadA5	0/0	100	100.0	NG_047357.1	ANT(3’’)-Ia family aminoglycoside nucleotidyltransferase AadA5	STREPTOMYCIN
contig00087	738	1565	aph(3’’)-Ib	0/0	100	100.0	NG_056002.2	aminoglycoside O-phosphotransferase APH(3’’)-Ib	STREPTOMYCIN
contig00092	1225	2100	blaCTX-M-15	0/0	100	100.0	NG_048935.1	class A extended-spectrum beta-lactamase CTX-M-15	CEPHALOSPORIN
contig00007	38239	39372	blaEC-15	0/0	100	98.5	NG_049081.1	class C extended-spectrum beta-lactamase EC-15	CEPHALOSPORIN
contig00106	578	1408	blaOXA-1	0/0	100	100.0	NG_049392.1	oxacillin-hydrolyzing class D beta-lactamase OXA-1	CEPHALOSPORIN
contig00087	3920	4780	blaTEM-1	0/0	100	100.0	NG_050145.1	class A broad-spectrum beta-lactamase TEM-1	BETA-LACTAM
contig00091	2692	3165	dfrA17	0/0	100	99.8	NG_047710.1	trimethoprim-resistant dihydrofolate reductase DfrA17	TRIMETHOPRIM
contig00091	387	1226	sul1	0/0	100	100.0	NG_048082.1	sulfonamide-resistant dihydropteroate synthase Sul1	SULFONAMIDE
contig00087	1602	2417	sul2	0/0	100	100.0	NG_051852.1	sulfonamide-resistant dihydropteroate synthase Sul2	SULFONAMIDE
contig00096	636	1841	tet(B)	0/0	100	99.9	NG_048163.1	tetracycline efflux MFS transporter Tet(B)	TETRACYCLINE

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00008	37540	38733	ACRA	0/0	100.0	100.0	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00008	38756	41905	ACRB	0/0	100.0	100.0	MEG_401	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRB	NA
contig00006	148083	151196	ACRD	0/0	100.0	98.8	MEG_407	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ACRD	NA
contig00072	5854	8958	ACRF	0/0	100.0	100.0	MEG_409	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRF	NA
contig00036	601	1263	ACRS	0/0	100.0	100.0	MEG_415	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS	NA
contig00008	126872	128029	AMPH	0/0	100.0	100.0	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00091	1773	2561	ANT3-DPRIME	0/0	100.0	100.0	MEG_928	Drugs:Aminoglycosides:Aminoglycoside_O-nucleotidyltransferases:ANT3-DPRIME	NA
contig00087	738	1565	APH3-DPRIME	0/0	100.0	100.0	MEG_1019	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH3-DPRIME	NA
contig00023	32871	34723	ASMA	0/0	100.0	97.2	MEG_1180	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:ASMA	NA
contig00003	70354	71173	BACA	0/0	99.8	98.8	MEG_1189	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00023	57249	57971	BAER	0/0	100.0	99.0	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00023	55849	57252	BAES	0/0	100.0	98.7	MEG_1193	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES	NA
contig00019	67340	68530	BCR	0/0	100.0	99.9	MEG_1210	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR	NA
contig00007	38239	39372	BLAEC	0/0	100.0	98.5	MEG_1282	Drugs:betalactams:Class_C_betalactamases:BLAEC	NA
contig00012	60881	61579	CPXAR	0/0	100.0	100.0	MEG_2122	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00012	61576	62949	CPXAR	0/0	100.0	100.0	MEG_2121	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00009	15081	15713	CRP	0/0	100.0	99.7	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00122	62	1004	CTX	0/0	100.0	98.2	MEG_2435	Drugs:betalactams:Class_A_betalactamases:CTX	NA
contig00091	2692	3165	DFRA	0/0	100.0	100.0	MEG_2547	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00010	58703	59875	EMRA	0/0	100.0	97.9	MEG_2722	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA	NA
contig00010	59892	61430	EMRB	0/0	100.0	98.6	MEG_2725	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRB	NA
contig00020	611	1801	EMRD	0/0	100.0	100.0	MEG_2729	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD	NA
contig00005	168194	169357	EMRK	0/0	100.0	98.2	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig00010	58046	58576	EMRR	0/0	100.0	99.4	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00005	166656	168194	EMRY	0/0	100.0	97.7	MEG_2736	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRY	NA
contig00007	81600	83243	EPTA	0/0	100.0	99.9	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig00005	170392	173985	EVGS	0/0	100.0	97.2	MEG_2869	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EVGS	NA
contig00042	1784	2512	GADW	0/0	100.0	100.0	MEG_3081	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig00042	592	1416	GADX	0/0	100.0	100.0	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00011	41423	41836	HNS	0/0	100.0	99.3	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00013	8127	8804	KDPE	0/0	100.0	100.0	MEG_3448	Drugs:Aminoglycosides:Aminoglycoside_efflux_pumps:KDPE	NA
contig00004	184592	184981	MARA	0/0	100.0	100.0	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00004	184995	185429	MARR	0/0	100.0	100.0	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00001	150954	152186	MDFA	0/0	100.0	100.0	MEG_3737	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDFA	NA
contig00023	46989	48236	MDTA	0/0	100.0	98.1	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00023	48236	51358	MDTB	0/0	100.0	99.9	MEG_3747	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTB	NA
contig00023	51359	54436	MDTC	0/0	100.0	97.7	MEG_3749	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTC	NA
contig00042	6013	7170	MDTE	0/0	100.0	100.0	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00042	2875	5988	MDTF	0/0	100.0	100.0	MEG_3752	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTF	NA
contig00034	18580	19806	MDTG	0/0	100.0	100.0	MEG_3753	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig00034	28435	29643	MDTH	0/0	100.0	99.9	MEG_3755	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTH	NA
contig00004	151870	152199	MDTI	0/0	100.0	100.0	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00004	151518	151883	MDTJ	0/0	100.0	99.5	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00004	80116	81489	MDTK	0/0	100.0	100.0	MEG_3759	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:MDTK	NA
contig00021	70066	71298	MDTM	0/0	100.0	96.3	MEG_3761	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTM	NA
contig00007	112981	114012	MDTN	0/0	100.0	100.0	MEG_3763	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN	NA
contig00007	114012	116063	MDTO	0/0	100.0	100.0	MEG_3764	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTO	NA
contig00007	116060	117526	MDTP	0/0	100.0	100.0	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig00006	126902	127376	MPHB	0/0	99.6	96.2	MEG_4033	Drugs:MLS:Macrolide_phosphotransferases:MPHB	NA
contig00001	233901	235649	MSBA	0/0	100.0	100.0	MEG_4061	Drugs:Multi-drug_resistance:Multi-drug_ABC_efflux_pumps:MSBA	NA
contig00106	578	1408	OXA	0/0	100.0	100.0	MEG_4980	Drugs:betalactams:Class_D_betalactamases:OXA	NA
contig00013	60214	62115	PBP2	0/0	100.0	100.0	MEG_5400	Drugs:betalactams:Penicillin_binding_protein:PBP2	NA
contig00049	28099	29397	PBP4B	0/0	99.5	96.1	MEG_5409	Drugs:betalactams:Penicillin_binding_protein:PBP4B	NA
contig00005	63989	64957	PMRF	0/0	100.0	98.0	MEG_5801	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF	NA
contig00021	21724	22593	ROBA	0/0	100.0	99.0	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00007	139143	139466	SOXS	0/0	100.0	100.0	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00091	260	1227	SULI	0/0	100.0	100.0	MEG_6615	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULI	NA
contig00087	1602	2417	SULII	0/0	100.0	100.0	MEG_6617	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULII	NA
contig00096	636	1841	TETB	0/0	100.0	99.9	MEG_7052	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETB	NA
contig00112	137	553	TETD	0/0	100.0	100.0	MEG_7070	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETD	NA
contig00005	2113	3756	YOGI	0/0	100.0	100.0	MEG_7842	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:YOGI	NA

ID169

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00090	1694	2554	aac(3)-IIa_1	0/0	100.0	99.8	X51534	aac(3)-IIa	Gentamicin, Tobramycin
contig00096	1540	2139	aac(6’)-Ib-cr_1	0/0	100.0	100.0	DQ303918	aac(6’)-Ib-cr	Ciprofloxacin
contig00072	1308	2096	aadA5_1	0/0	100.0	100.0	AF137361	aadA5	Streptomycin
contig00087	912	1715	aph(3’’)-Ib_5	0/0	100.0	100.0	AF321551	aph(3’’)-Ib	Streptomycin
contig00087	76	912	aph(6)-Id_1	0/0	100.0	99.9	M28829	aph(6)-Id	Streptomycin
contig00074	2407	3282	blaCTX-M-15_1	0/0	100.0	100.0	AY044436	blaCTX-M-15	Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig00096	579	1409	blaOXA-1_1	0/0	100.0	100.0	HQ170510	blaOXA-1	Amoxicillin, Amoxicillin+Clavulanic_acid, Ampicillin, Ampicillin+Clavulanic_acid, Cefepime, Piperacillin, Piperacillin+Tazobactam
contig00072	704	1177	dfrA17_1	0/0	100.0	100.0	FJ460238	dfrA17	Trimethoprim
contig00001	29919	31151	mdf(A)_1	0/0	100.0	97.8	Y08743	mdf(A)
contig00111	69	907	mph(A)_1	0/0	92.6	100.0	D16251	mph(A)	Erythromycin, Azithromycin, Spiramycin, Telithromycin
contig00072	2616	3482	sul1_5	0/0	100.0	99.9	EU780013	sul1	Sulfamethoxazole
contig00087	1776	2591	sul2_2	0/0	100.0	100.0	AY034138	sul2	Sulfamethoxazole
contig00073	5808	7054	tet(A)_6	0/0	97.8	100.0	AF534183	tet(A)	Doxycycline, Tetracycline

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00090	1694	2554	AAC(3)-IIe	0/0	100.0	99.5	EU022315.1:0-861	AAC(3)-IIe is a plasmid-encoded aminoglycoside acetyltransferase in E. coli	aminoglycoside
contig00096	1540	2139	AAC(6’)-Ib-cr	0/0	100.0	100.0	DQ303918:0-600	AAC(6’)-Ib-cr is an aminoglycoside acetyltransferase encoded by plasmids transposons integrons in Enterobacteriaceae. The aac(6’)-Ib-cr variant gene can induce resistance against aminoglycoside and fluoroquinolone simultaneously	aminoglycoside, fluoroquinolone
contig00072	1308	2096	aadA5	0/0	100.0	100.0	AF137361:63-852	aadA5 is an aminoglycoside nucleotidyltransferase gene encoded by plasmids transposons and integrons in E. coli K. pneumoniae Kluyvera georgiana P. aeruginosa and E. cloacae	aminoglycoside
contig00005	43328	46477	acrB	0/0	100.0	98.8	U00096.3:484403-481253	Protein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug/proton antiporter.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00003	132237	135350	acrD	0/0	100.0	98.7	AP009048.1:2586250-2589364	AcrD is an aminoglycoside efflux pump expressed in E. coli. Its expression can be induced by indole and is regulated by baeRS and cpxAR.	aminoglycoside
contig00010	149301	150458	acrE	0/0	100.0	98.8	U00096:3413863-3415021	AcrE is a membrane fusion protein similar to AcrA.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00010	150470	153574	acrF	0/0	100.0	96.6	U00096:3415032-3418137	AcrF is a inner membrane transporter similar to AcrB.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00010	148240	148902	acrS	0/0	100.0	98.3	U00096:3413465-3412802	AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.	cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00087	912	1715	APH(3’’)-Ib	0/0	100.0	99.8	AF313472:15593-16397	APH(3’’)-Ib is an aminoglycoside phosphotransferase encoded by plasmids transposons integrative conjugative elements and chromosomes in Enterobacteriaceae and Pseudomonas spp.	aminoglycoside
contig00087	76	912	APH(6)-Id	0/0	100.0	99.8	AF024602:3155-3992	APH(6)-Id is an aminoglycoside phosphotransferase encoded by plasmids integrative conjugative elements and chromosomal genomic islands in K. pneumoniae Salmonella spp. E. coli Shigella flexneri Providencia alcalifaciens Pseudomonas spp. V. cholerae Edwardsiella tarda Pasteurella multocida and Aeromonas bestiarum	aminoglycoside
contig00008	120355	121174	bacA	0/0	99.8	98.3	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00004	169403	170124	baeR	0/0	99.9	97.1	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00004	170121	171524	baeS	0/0	100.0	90.5	AP009048:2165012-2166416	BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.	aminocoumarin, aminoglycoside
contig00019	66690	68057	cpxA	0/0	99.6	98.5	BA000007.3:4905062-4903688	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	aminocoumarin, aminoglycoside
contig00006	15089	15721	CRP	0/0	100.0	99.2	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00074	2407	3282	CTX-M-15	0/0	100.0	100.0	AY044436:1435-2311	CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family	cephalosporin
contig00072	704	1177	dfrA17	0/0	100.0	100.0	DQ838665:0-474	dfrA17 is an integron-encoded dihydrofolate reductase found in Escherichia coli	diaminopyrimidine
contig00055	7374	8546	emrA	0/0	100.0	98.0	AP009048:2810082-2811255	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	fluoroquinolone
contig00055	5819	7357	emrB	0/0	100.0	98.4	U00096:2812615-2814154	emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin.	fluoroquinolone
contig00003	38467	39522	emrK	0/0	100.0	97.7	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00055	8673	9203	emrR	0/0	100.0	98.5	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00003	36929	38467	emrY	0/0	100.0	97.7	D78168:1591-3130	emrY is a multidrug transport that moves substrates across the inner membrane of the Gram-negative E. coli. It is a homolog of emrB.	tetracycline
contig00035	18414	20057	eptA	0/0	100.0	91.4	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00005	42112	43305	Escherichia_coli_acrA	0/0	100.0	99.1	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00022	48091	49224	Escherichia_coli_ampC	0/0	100.0	97.8	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00005	131227	132384	Escherichia_coli_ampH	0/0	100.0	97.1	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig00016	28735	29067	Escherichia_coli_emrE	0/0	100.0	92.2	Z11877.1:485-818	Member of the small MDR (multidrug resistance) family of transporters, in Escherichia coli this protein provides resistance against a number of positively charged compounds including ethidium bromide and erythromycin, proton-dependent secondary transporter which exchanges protons for compound translocation	macrolide
contig00001	29919	31151	Escherichia_coli_mdfA	0/0	100.0	96.3	JQ394987:0-1233	Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter.	benzalkonium_chloride, rhodamine, tetracycline
contig00003	40046	40660	evgA	0/0	100.0	99.0	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00003	40665	44258	evgS	0/0	100.0	96.3	U00096:2484373-2487967	EvgS is a sensor protein that phosphorylates the regulatory protein EvgA. evgS corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	fluoroquinolone, macrolide, penam, tetracycline
contig00006	188688	189416	gadW	0/0	100.0	100.0	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig00006	189785	190609	gadX	0/0	100.0	93.9	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00021	34762	35175	H-NS	0/0	100.0	99.3	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00001	185272	185944	kdpE	0/0	99.3	95.5	U00096.3:721733-721055	kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding.	aminoglycoside
contig00031	29733	30116	marA	0/0	100.0	99.0	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00004	179137	180384	mdtA	0/0	100.0	95.6	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00004	176015	179137	mdtB	0/0	100.0	96.2	U00096:2155262-2158385	MdtB is a transporter that forms a heteromultimer complex with MdtC to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex.	aminocoumarin
contig00004	172937	176014	mdtC	0/0	100.0	94.0	U00096:2158385-2161463	MdtC is a transporter that forms a heteromultimer complex with MdtB to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex. In the absence of MdtB MdtC can form a homomultimer complex that results in a functioning efflux complex with a narrower drug specificity. mdtC corresponds to 3 loci in Pseudomonas aeruginosa PAO1 (gene name: muxC/muxB) and 3 loci in Pseudomonas aeruginosa LESB58.	aminocoumarin
contig00006	184030	185187	mdtE	0/0	100.0	98.5	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00006	185212	188325	mdtF	0/0	100.0	97.3	U00096:3660413-3663527	MdtF is the multidrug inner membrane transporter for the MdtEF-TolC efflux complex.	fluoroquinolone, macrolide, penam
contig00032	2460	3686	mdtG	0/0	100.0	98.4	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00020	6127	7335	mdtH	0/0	100.0	98.3	U00096:1125326-1124117	Multidrug resistance protein MdtH	fluoroquinolone
contig00027	38804	40036	mdtM	0/0	100.0	95.0	U00096.3:4568519-4567286	Multidrug resistance protein MdtM	acridine_dye, fluoroquinolone, lincosamide, nucleoside, phenicol
contig00013	10778	11809	mdtN	0/0	100.0	96.2	AP009048.1:4307588-4306556	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	acridine_dye, nucleoside
contig00013	11809	13860	mdtO	0/0	100.0	97.0	AP009048.1:4306557-4304505	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00013	13857	15323	mdtP	0/0	100.0	97.6	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00111	69	907	mphA	0/0	92.6	100.0	D16251.1:2531-1625	The mphA gene encodes for resistance enzyme MPH(2’)-I which preferentially inactivate 14-membered macrolides (e.g.erythromycin telithromycin roxithromycin) over 16-membered macrolides (e.g.tylosin spiramycin). It phosphorylates macrolides at 2’-OH hydroxyl of desosamine sugar of macrolides in a GTP-dependent manner.	macrolide
contig00011	45414	47162	msbA	0/0	100.0	98.1	U00096.3:966620-968369	MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability.	nitroimidazole
contig00096	579	1409	OXA-1	0/0	100.0	100.0	JN420336.1:2230-1399	OXA-1 is a beta-lactamase found in E. coli	cephalosporin, penam
contig00012	63603	64571	pmrF	0/0	100.0	97.6	U00096:2367070-2368039	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide
contig00072	2643	3482	sul1	0/0	100.0	100.0	JF969163:1053-1893	Sul1 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria. It is linked to other resistance genes of class 1 integrons.	sulfonamide
contig00087	1776	2591	sul2	0/0	100.0	100.0	AY055428.1:21084-20268	Sul2 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria usually found on small plasmids.	sulfonamide
contig00073	5808	7054	tet(A)	0/0	97.8	100.0	AF534183.1:2970-4245	TetA is a tetracycline efflux pump found in many species of Gram-negative bacteria.	tetracycline
contig00008	93185	94672	tolC	0/0	100.0	98.2	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan
contig00004	233480	234646	ugd	0/0	100.0	96.0	U00096:2099613-2098446	PmrE is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin	peptide
contig00012	3755	5398	yojI	0/0	100.0	97.4	U00096.3:2308615-2306971	YojI mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. YojI is capable of pumping out microcin molecules. The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI.	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00090	1694	2554	(AGly)aac3-IIa	0/0	100.0	99.8	X51534:91-951	(AGly)aac3-IIa	NA
contig00072	1308	2096	(AGly)aadA5	0/0	100.0	100.0	AF137361:64-852	(AGly)aadA5	NA
contig00087	912	1715	(AGly)strA	0/0	100.0	99.9	AB366441:22458-23261	(AGly)strA	NA
contig00087	76	912	(AGly)strB	0/0	100.0	99.9	FJ474091:264-1100	(AGly)strB	NA
contig00022	48091	49224	(Bla)AmpC2_Ecoli	0/0	100.0	97.8	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00005	131227	132384	(Bla)ampH_Ecoli	0/0	100.0	97.1	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00074	2407	3282	(Bla)blaCTX-M-15	0/0	100.0	100.0	JQ686199:261-1136	(Bla)blaCTX-M-15	NA
contig00096	579	1409	(Bla)blaOXA-1	0/0	100.0	100.0	JQ682867:1-831	(Bla)blaOXA-1	NA
contig00001	244490	246391	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100.0	98.7	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA
contig00111	69	907	(MLS)mph(A)	0/0	92.6	100.0	DQ445270:1626-2531	(MLS)mph(A)	NA
contig00072	2643	3482	(Sul)sul1	0/0	100.0	100.0	AF071413:6700-7539	(Sul)sul1	NA
contig00087	1776	2591	(Sul)sul2	0/0	100.0	100.0	EU360945:1617-2432	(Sul)sul2	NA
contig00073	5780	7054	(Tet)tetA	0/0	100.0	100.0	JX424423:94438-95712	(Tet)tetA	NA
contig00072	704	1177	(Tmt)dfrA17	0/0	100.0	100.0	AB126604:98-571	(Tmt)dfrA17	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00090	1694	2554	aac(3)-IIe	0/0	100.0	99.8	NG_047244.1	aminoglycoside N-acetyltransferase AAC(3)-IIe	GENTAMICIN
contig00096	1540	2094	aac(6’)-Ib-D181Y	0/0	100.0	99.8	NG_067946.1	AAC(6’)-Ib family aminoglycoside 6’-N-acetyltransferase	AMIKACIN, KANAMYCIN, TOBRAMYCIN
contig00072	1308	2096	aadA5	0/0	100.0	100.0	NG_047357.1	ANT(3’’)-Ia family aminoglycoside nucleotidyltransferase AadA5	STREPTOMYCIN
contig00087	912	1739	aph(3’’)-Ib	0/0	100.0	100.0	NG_056002.2	aminoglycoside O-phosphotransferase APH(3’’)-Ib	STREPTOMYCIN
contig00087	76	912	aph(6)-Id	0/0	100.0	100.0	NG_047466.1	aminoglycoside O-phosphotransferase APH(6)-Id	STREPTOMYCIN
contig00074	2407	3282	blaCTX-M-15	0/0	100.0	100.0	NG_048935.1	class A extended-spectrum beta-lactamase CTX-M-15	CEPHALOSPORIN
contig00022	48091	49224	blaEC-5	0/0	100.0	99.5	NG_049085.1	cephalosporin-hydrolyzing class C beta-lactamase EC-5	CEPHALOSPORIN
contig00096	579	1409	blaOXA-1	0/0	100.0	100.0	NG_049392.1	oxacillin-hydrolyzing class D beta-lactamase OXA-1	CEPHALOSPORIN
contig00072	704	1177	dfrA17	0/0	100.0	99.8	NG_047710.1	trimethoprim-resistant dihydrofolate reductase DfrA17	TRIMETHOPRIM
contig00111	69	907	mph(A)	0/0	92.6	100.0	NG_047985.1	Mph(A) family macrolide 2’-phosphotransferase	MACROLIDE
contig00072	2643	3482	sul1	0/0	100.0	100.0	NG_048082.1	sulfonamide-resistant dihydropteroate synthase Sul1	SULFONAMIDE
contig00087	1776	2591	sul2	0/0	100.0	100.0	NG_051852.1	sulfonamide-resistant dihydropteroate synthase Sul2	SULFONAMIDE
contig00073	5780	6979	tet(A)	0/0	100.0	100.0	NG_048154.1	tetracycline efflux MFS transporter Tet(A)	TETRACYCLINE

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00090	1694	2554	AAC3	0/0	100.0	99.8	MEG_44	Drugs:Aminoglycosides:Aminoglycoside_N-acetyltransferases:AAC3	NA
contig00005	42112	43305	ACRA	0/0	100.0	99.1	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00005	43328	46477	ACRB	0/0	100.0	98.8	MEG_401	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRB	NA
contig00003	132237	135350	ACRD	0/0	100.0	98.7	MEG_407	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ACRD	NA
contig00010	149301	150458	ACRE	0/0	100.0	98.8	MEG_408	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRE	NA
contig00010	150470	153574	ACRF	0/0	100.0	96.6	MEG_409	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRF	NA
contig00010	148240	148902	ACRS	0/0	100.0	98.3	MEG_415	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS	NA
contig00005	131227	132384	AMPH	0/0	100.0	97.1	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00072	1308	2096	ANT3-DPRIME	0/0	100.0	100.0	MEG_928	Drugs:Aminoglycosides:Aminoglycoside_O-nucleotidyltransferases:ANT3-DPRIME	NA
contig00087	912	1739	APH3-DPRIME	0/0	100.0	100.0	MEG_1019	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH3-DPRIME	NA
contig00087	76	912	APH6	0/0	100.0	100.0	MEG_1084	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH6	NA
contig00004	192044	193896	ASMA	0/0	100.0	97.6	MEG_1180	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:ASMA	NA
contig00008	120355	121174	BACA	0/0	99.8	98.5	MEG_1189	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00004	169403	170124	BAER	0/0	99.9	97.1	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00004	170121	171524	BAES	0/0	100.0	90.5	MEG_1193	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES	NA
contig00004	19847	21037	BCR	0/0	100.0	96.6	MEG_1210	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR	NA
contig00022	48091	49224	BLAEC	0/0	100.0	99.5	MEG_1275	Drugs:betalactams:Class_C_betalactamases:BLAEC	NA
contig00019	65995	66693	CPXAR	0/0	100.0	98.1	MEG_2118	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00019	66690	68057	CPXAR	0/0	99.6	99.0	MEG_2121	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00006	15089	15721	CRP	0/0	100.0	99.2	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00072	704	1177	DFRA	0/0	100.0	100.0	MEG_2547	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00055	7374	8546	EMRA	0/0	100.0	98.0	MEG_2722	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA	NA
contig00055	5819	7357	EMRB	0/0	100.0	98.4	MEG_2725	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRB	NA
contig00002	194231	195421	EMRD	0/0	100.0	97.5	MEG_2729	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD	NA
contig00003	38467	39630	EMRK	0/0	100.0	97.4	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig00055	8673	9203	EMRR	0/0	100.0	98.5	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00003	36929	38467	EMRY	0/0	100.0	97.7	MEG_2736	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRY	NA
contig00035	18414	20057	EPTA	0/0	100.0	91.4	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig00003	40665	44258	EVGS	0/0	100.0	97.4	MEG_2869	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EVGS	NA
contig00006	188688	189416	GADW	0/0	100.0	100.0	MEG_3082	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig00006	189785	190609	GADX	0/0	100.0	93.9	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00021	34762	35175	HNS	0/0	100.0	99.3	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00001	185272	185944	KDPE	0/0	99.3	95.5	MEG_3448	Drugs:Aminoglycosides:Aminoglycoside_efflux_pumps:KDPE	NA
contig00031	29727	30116	MARA	0/0	100.0	99.0	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00031	29278	29712	MARR	0/0	100.0	98.2	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00001	29919	31151	MDFA	0/0	100.0	97.9	MEG_3737	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDFA	NA
contig00004	179137	180384	MDTA	0/0	100.0	95.6	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00004	176015	179137	MDTB	0/0	100.0	96.2	MEG_3747	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTB	NA
contig00004	172937	176014	MDTC	0/0	100.0	94.0	MEG_3749	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTC	NA
contig00006	184030	185187	MDTE	0/0	100.0	98.5	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00006	185212	188325	MDTF	0/0	100.0	97.3	MEG_3752	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTF	NA
contig00032	2460	3686	MDTG	0/0	100.0	98.5	MEG_3753	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig00020	6127	7335	MDTH	0/0	100.0	98.3	MEG_3755	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTH	NA
contig00036	35469	35798	MDTI	0/0	100.0	98.8	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00036	35117	35482	MDTJ	0/0	100.0	98.4	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00024	70531	71903	MDTK	0/0	99.9	97.7	MEG_3759	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:MDTK	NA
contig00027	38804	40036	MDTM	0/0	100.0	95.0	MEG_3761	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTM	NA
contig00013	10778	11809	MDTN	0/0	100.0	96.2	MEG_3763	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN	NA
contig00013	11809	13860	MDTO	0/0	100.0	97.0	MEG_3764	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTO	NA
contig00013	13857	15323	MDTP	0/0	100.0	97.6	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig00111	69	907	MPHA	0/0	92.6	100.0	MEG_4029	Drugs:MLS:Macrolide_phosphotransferases:MPHA	NA
contig00011	45414	47162	MSBA	0/0	100.0	98.1	MEG_4061	Drugs:Multi-drug_resistance:Multi-drug_ABC_efflux_pumps:MSBA	NA
contig00016	28735	29067	MVRC	0/0	100.0	92.2	MEG_4103	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MVRC	NA
contig00096	579	1409	OXA	0/0	100.0	100.0	MEG_4980	Drugs:betalactams:Class_D_betalactamases:OXA	NA
contig00001	244490	246391	PBP2	0/0	100.0	98.7	MEG_5400	Drugs:betalactams:Penicillin_binding_protein:PBP2	NA
contig00012	63603	64571	PMRF	0/0	100.0	97.6	MEG_5801	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF	NA
contig00030	37224	38093	ROBA	0/0	100.0	99.0	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00013	43354	43676	SOXS	0/0	99.7	98.1	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00072	2642	3609	SULI	0/0	100.0	100.0	MEG_6615	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULI	NA
contig00087	1776	2591	SULII	0/0	100.0	100.0	MEG_6617	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULII	NA
contig00073	5780	7054	TETA	0/0	100.0	100.0	MEG_7024	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETA	NA
contig00004	233480	234646	UGD	0/0	100.0	96.0	MEG_7328	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:UGD	NA
contig00012	3755	5398	YOGI	0/0	100.0	97.4	MEG_7842	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:YOGI	NA

ID177

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00070	1578	2381	aph(3’’)-Ib_5	0/0	100.0	100.0	AF321551	aph(3’’)-Ib	Streptomycin
contig00070	742	1578	aph(6)-Id_1	0/0	100.0	100.0	M28829	aph(6)-Id	Streptomycin
contig00052	6580	7455	blaCTX-M-15_1	0/0	100.0	100.0	AY044436	blaCTX-M-15	Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig00080	220	1032	blaNDM-5_1	0/0	100.0	100.0	JN104597	blaNDM-5	Amoxicillin, Amoxicillin+Clavulanic_acid, Ampicillin, Ampicillin+Clavulanic_acid, Cefepime, Cefixime, Cefotaxime, Cefoxitin, Ceftazidime, Ertapenem, Imipenem, Meropenem, Piperacillin, Piperacillin+Tazobactam
contig00052	2899	3759	blaTEM-1B_1	0/0	100.0	100.0	AY458016	blaTEM-1B	Amoxicillin, Ampicillin, Cephalothin, Piperacillin, Ticarcillin
contig00073	181	663	dfrA14_5	0/0	100.0	99.6	DQ388123	dfrA14	Trimethoprim
contig00014	32376	33608	mdf(A)_1	0/0	100.0	98.1	Y08743	mdf(A)
contig00057	5278	5934	qnrS1_1	0/0	100.0	100.0	AB187515	qnrS1	Ciprofloxacin
contig00070	2442	3257	sul2_2	0/0	100.0	100.0	AY034138	sul2	Sulfamethoxazole
contig00052	317	1563	tet(A)_6	0/0	97.8	100.0	AF534183	tet(A)	Doxycycline, Tetracycline

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00033	12982	16131	acrB	0/0	100.0	99.0	U00096.3:484403-481253	Protein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug/proton antiporter.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00011	134717	137830	acrD	0/0	100.0	98.8	AP009048.1:2586250-2589364	AcrD is an aminoglycoside efflux pump expressed in E. coli. Its expression can be induced by indole and is regulated by baeRS and cpxAR.	aminoglycoside
contig00008	163230	164387	acrE	0/0	100.0	98.4	U00096:3413863-3415021	AcrE is a membrane fusion protein similar to AcrA.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00008	164399	167503	acrF	0/0	100.0	97.8	U00096:3415032-3418137	AcrF is a inner membrane transporter similar to AcrB.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00008	162169	162831	acrS	0/0	100.0	98.9	U00096:3413465-3412802	AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.	cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00070	1578	2381	APH(3’’)-Ib	0/0	100.0	99.8	AF313472:15593-16397	APH(3’’)-Ib is an aminoglycoside phosphotransferase encoded by plasmids transposons integrative conjugative elements and chromosomes in Enterobacteriaceae and Pseudomonas spp.	aminoglycoside
contig00070	742	1578	APH(6)-Id	0/0	100.0	99.9	AF024602:3155-3992	APH(6)-Id is an aminoglycoside phosphotransferase encoded by plasmids integrative conjugative elements and chromosomal genomic islands in K. pneumoniae Salmonella spp. E. coli Shigella flexneri Providencia alcalifaciens Pseudomonas spp. V. cholerae Edwardsiella tarda Pasteurella multocida and Aeromonas bestiarum	aminoglycoside
contig00007	138999	139818	bacA	0/0	99.8	96.2	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00026	11097	11819	baeR	0/0	100.0	99.3	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00026	11816	13219	baeS	0/0	100.0	99.6	AP009048:2165012-2166416	BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.	aminocoumarin, aminoglycoside
contig00029	38790	40163	cpxA	0/0	100.0	98.6	BA000007.3:4905062-4903688	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	aminocoumarin, aminoglycoside
contig00016	15391	16023	CRP	0/0	100.0	99.0	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00052	6580	7455	CTX-M-15	0/0	100.0	100.0	AY044436:1435-2311	CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family	cephalosporin
contig00080	1036	1401	determinant_of_bleomycin_resistance	0/0	100.0	100.0	KC503911.1:9883-10249	A novel bleomycin resistance protein encoded by a metallo-beta-lactamase-associated ble gene. Expression of BRP(MBL) confers resistance to bleomycin and bleomycin-like antibiotics in Enterobacteriaceae and Acinetobacter where it is co-expressed with an MBL and controlled by the same promoter region.	glycopeptide
contig00073	181	663	dfrA14	0/0	100.0	99.8	EU780012:2162-2645	dfrA14 is an integron-encoded dihydrofolate reductase found in Escherichia coli	diaminopyrimidine
contig00012	60401	61573	emrA	0/0	100.0	98.0	AP009048:2810082-2811255	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	fluoroquinolone
contig00012	61590	63128	emrB	0/0	100.0	98.0	U00096:2812615-2814154	emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin.	fluoroquinolone
contig00001	338432	339487	emrK	0/0	100.0	97.8	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00012	59744	60274	emrR	0/0	100.0	99.4	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00001	336894	338432	emrY	0/0	100.0	97.5	D78168:1591-3130	emrY is a multidrug transport that moves substrates across the inner membrane of the Gram-negative E. coli. It is a homolog of emrB.	tetracycline
contig00004	67358	69001	eptA	0/0	100.0	98.2	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00033	16154	17347	Escherichia_coli_acrA	0/0	100.0	99.2	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00004	110920	112053	Escherichia_coli_ampC	0/0	100.0	97.7	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00001	401770	403074	Escherichia_coli_ampC1_beta-lactamase	0/0	100.0	96.0	FN649414.1:2765050-2766355	An ampC-like beta-lactamase identified from Escherichia coli.	cephalosporin, penam
contig00009	24731	25888	Escherichia_coli_ampH	0/0	100.0	96.9	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig00014	32376	33608	Escherichia_coli_mdfA	0/0	100.0	96.6	JQ394987:0-1233	Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter.	benzalkonium_chloride, rhodamine, tetracycline
contig00001	340011	340625	evgA	0/0	100.0	99.0	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00065	316	930	evgA	0/0	100.0	98.5	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00001	340630	344223	evgS	0/0	100.0	96.8	U00096:2484373-2487967	EvgS is a sensor protein that phosphorylates the regulatory protein EvgA. evgS corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	fluoroquinolone, macrolide, penam, tetracycline
contig00065	935	4528	evgS	0/0	100.0	95.9	U00096:2484373-2487967	EvgS is a sensor protein that phosphorylates the regulatory protein EvgA. evgS corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	fluoroquinolone, macrolide, penam, tetracycline
contig00010	54226	54954	gadW	0/0	100.0	95.6	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig00010	55323	56147	gadX	0/0	100.0	94.2	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00006	22689	23102	H-NS	0/0	100.0	99.5	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00015	7853	8530	kdpE	0/0	100.0	95.4	U00096.3:721733-721055	kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding.	aminoglycoside
contig00017	78088	78471	marA	0/0	100.0	99.5	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00026	20832	22079	mdtA	0/0	100.0	98.2	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00026	17710	20832	mdtB	0/0	100.0	98.0	U00096:2155262-2158385	MdtB is a transporter that forms a heteromultimer complex with MdtC to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex.	aminocoumarin
contig00026	14632	17709	mdtC	0/0	100.0	98.1	U00096:2158385-2161463	MdtC is a transporter that forms a heteromultimer complex with MdtB to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex. In the absence of MdtB MdtC can form a homomultimer complex that results in a functioning efflux complex with a narrower drug specificity. mdtC corresponds to 3 loci in Pseudomonas aeruginosa PAO1 (gene name: muxC/muxB) and 3 loci in Pseudomonas aeruginosa LESB58.	aminocoumarin
contig00010	49568	50725	mdtE	0/0	100.0	98.8	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00010	50750	53863	mdtF	0/0	100.0	98.5	U00096:3660413-3663527	MdtF is the multidrug inner membrane transporter for the MdtEF-TolC efflux complex.	fluoroquinolone, macrolide, penam
contig00005	44635	45861	mdtG	0/0	100.0	98.5	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00005	34796	36004	mdtH	0/0	100.0	97.8	U00096:1125326-1124117	Multidrug resistance protein MdtH	fluoroquinolone
contig00002	284727	285959	mdtM	0/0	100.0	96.5	U00096.3:4568519-4567286	Multidrug resistance protein MdtM	acridine_dye, fluoroquinolone, lincosamide, nucleoside, phenicol
contig00004	43659	44690	mdtN	0/0	100.0	96.4	AP009048.1:4307588-4306556	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	acridine_dye, nucleoside
contig00004	41608	43659	mdtO	0/0	100.0	96.3	AP009048.1:4306557-4304505	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00004	40145	41611	mdtP	0/0	100.0	97.5	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00011	113536	114010	mphB	0/0	99.6	96.6	AE005174.2:3397370-3397847	The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides.	macrolide
contig00005	179254	181002	msbA	0/0	100.0	99.0	U00096.3:966620-968369	MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability.	nitroimidazole
contig00080	220	1032	NDM-5	0/0	100.0	100.0	JN104597:114-927	New Delhi beta-lactamase NDM-5.	carbapenem, cephalosporin, cephamycin, penam
contig00001	194864	195832	pmrF	0/0	100.0	98.1	U00096:2367070-2368039	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide
contig00057	5278	5934	QnrS1	0/0	100.0	100.0	DQ485529.1:0-657	QnrS1 is a plasmid-mediated quinolone resistance protein found in Shigella flexneri	fluoroquinolone
contig00070	2442	3257	sul2	0/0	100.0	100.0	AY055428.1:21084-20268	Sul2 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria usually found on small plasmids.	sulfonamide
contig00052	2899	3759	TEM-1	0/0	100.0	99.9	AL513383:161910-162771	TEM-1 is a broad-spectrum beta-lactamase found in many Gram-negative bacteria. Confers resistance to penicillins and first generation cephalosphorins.	cephalosporin, monobactam, penam, penem
contig00052	317	1563	tet(A)	0/0	97.8	100.0	AF534183.1:2970-4245	TetA is a tetracycline efflux pump found in many species of Gram-negative bacteria.	tetracycline
contig00007	116800	118287	tolC	0/0	100.0	98.5	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan
contig00044	20936	22102	ugd	0/0	100.0	96.2	U00096:2099613-2098446	PmrE is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin	peptide
contig00001	131725	133368	yojI	0/0	100.0	97.5	U00096.3:2308615-2306971	YojI mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. YojI is capable of pumping out microcin molecules. The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI.	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00070	1578	2381	(AGly)strA	0/0	100	99.9	AB366441:22458-23261	(AGly)strA	NA
contig00070	742	1578	(AGly)strB	0/0	100	100.0	FJ474091:264-1100	(AGly)strB	NA
contig00001	401770	403074	(Bla)AmpC1_Ecoli	0/0	100	96.0	FN649414:2765051-2766355	(Bla)AmpC1_Ecoli	NA
contig00004	110920	112053	(Bla)AmpC2_Ecoli	0/0	100	97.7	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00009	24731	25888	(Bla)ampH_Ecoli	0/0	100	96.9	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00052	6580	7455	(Bla)blaCTX-M-15	0/0	100	100.0	JQ686199:261-1136	(Bla)blaCTX-M-15	NA
contig00080	220	1032	(Bla)blaNDM-5	0/0	100	100.0	JN104597:1-813	(Bla)blaNDM-5	NA
contig00052	2899	3759	(Bla)blaTEM-105	0/0	100	99.9	AF516720:215-1075	(Bla)blaTEM-105	NA
contig00015	50396	52297	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100	99.0	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA
contig00057	5278	5934	(Flq)qnr-S1	0/0	100	100.0	AB187515:9737-10393	(Flq)qnr-S1	NA
contig00070	2442	3257	(Sul)sul2	0/0	100	100.0	EU360945:1617-2432	(Sul)sul2	NA
contig00052	317	1591	(Tet)tetA	0/0	100	100.0	JX424423:94438-95712	(Tet)tetA	NA
contig00073	181	654	(Tmt)dfrA14	0/0	100	100.0	GU726917:72-545	(Tmt)dfrA14	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00070	1578	2405	aph(3’’)-Ib	0/0	100	100.0	NG_056002.2	aminoglycoside O-phosphotransferase APH(3’’)-Ib	STREPTOMYCIN
contig00070	742	1578	aph(6)-Id	0/0	100	100.0	NG_047464.1	aminoglycoside O-phosphotransferase APH(6)-Id	STREPTOMYCIN
contig00052	6580	7455	blaCTX-M-15	0/0	100	100.0	NG_048935.1	class A extended-spectrum beta-lactamase CTX-M-15	CEPHALOSPORIN
contig00004	110920	112053	blaEC-8	0/0	100	98.2	NG_049086.1	cephalosporin-hydrolyzing class C beta-lactamase EC-8	CEPHALOSPORIN
contig00080	220	1032	blaNDM-5	0/0	100	100.0	NG_049337.1	subclass B1 metallo-beta-lactamase NDM-5	CARBAPENEM
contig00052	2899	3759	blaTEM-1	0/0	100	100.0	NG_050145.1	class A broad-spectrum beta-lactamase TEM-1	BETA-LACTAM
contig00080	1036	1401	ble-MBL	0/0	100	100.0	NG_047559.1	bleomycin binding protein Ble-MBL	BLEOMYCIN
contig00073	181	654	dfrA14	0/0	100	100.0	NG_056035.1	trimethoprim-resistant dihydrofolate reductase DfrA14	TRIMETHOPRIM
contig00057	5278	5934	qnrS1	0/0	100	100.0	NG_050543.1	quinolone resistance pentapeptide repeat protein QnrS1	QUINOLONE
contig00070	2442	3257	sul2	0/0	100	100.0	NG_051852.1	sulfonamide-resistant dihydropteroate synthase Sul2	SULFONAMIDE
contig00052	392	1591	tet(A)	0/0	100	100.0	NG_048154.1	tetracycline efflux MFS transporter Tet(A)	TETRACYCLINE

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00033	16154	17347	ACRA	0/0	100.0	99.2	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00033	12982	16131	ACRB	0/0	100.0	99.0	MEG_401	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRB	NA
contig00011	134717	137830	ACRD	0/0	100.0	98.8	MEG_407	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ACRD	NA
contig00008	163230	164387	ACRE	0/0	100.0	98.4	MEG_408	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRE	NA
contig00008	164399	167503	ACRF	0/0	100.0	97.8	MEG_409	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRF	NA
contig00008	162169	162831	ACRS	0/0	100.0	98.9	MEG_415	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS	NA
contig00009	24731	25888	AMPH	0/0	100.0	96.9	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00070	1578	2405	APH3-DPRIME	0/0	100.0	100.0	MEG_1019	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH3-DPRIME	NA
contig00070	742	1578	APH6	0/0	100.0	100.0	MEG_1086	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH6	NA
contig00026	34014	35866	ASMA	0/0	100.0	98.4	MEG_1180	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:ASMA	NA
contig00007	138999	139818	BACA	0/0	99.8	96.7	MEG_1189	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00026	11097	11819	BAER	0/0	100.0	99.3	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00026	11816	13219	BAES	0/0	100.0	99.6	MEG_1193	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES	NA
contig00001	105265	106455	BCR	0/0	100.0	97.5	MEG_1210	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR	NA
contig00004	110920	112053	BLAEC	0/0	100.0	98.2	MEG_1278	Drugs:betalactams:Class_C_betalactamases:BLAEC	NA
contig00080	1036	1401	BRP	0/0	100.0	100.0	MEG_1477	Drugs:Glycopeptides:Bleomycin_resistance_protein:BRP	NA
contig00029	38790	40163	CPXAR	0/0	100.0	98.8	MEG_2121	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00029	40160	40858	CPXAR	0/0	100.0	99.4	MEG_2118	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00016	15391	16023	CRP	0/0	100.0	99.0	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00073	181	654	DFRA	0/0	100.0	99.8	MEG_2517	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00012	60401	61573	EMRA	0/0	100.0	98.0	MEG_2722	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA	NA
contig00012	61590	63128	EMRB	0/0	100.0	98.0	MEG_2725	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRB	NA
contig00037	24611	25801	EMRD	0/0	100.0	97.7	MEG_2729	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD	NA
contig00001	338432	339595	EMRK	0/0	100.0	98.0	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig00012	59744	60274	EMRR	0/0	100.0	99.4	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00001	336894	338432	EMRY	0/0	100.0	97.5	MEG_2736	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRY	NA
contig00004	67358	69001	EPTA	0/0	100.0	98.2	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig00001	340630	344223	EVGS	0/0	100.0	97.3	MEG_2869	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EVGS	NA
contig00065	935	4528	EVGS	0/0	100.0	97.0	MEG_2869	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EVGS	NA
contig00010	54226	54954	GADW	0/0	100.0	97.8	MEG_3081	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig00010	55323	56147	GADX	0/0	100.0	94.2	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00006	22689	23102	HNS	0/0	100.0	99.5	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00015	7853	8530	KDPE	0/0	100.0	95.4	MEG_3448	Drugs:Aminoglycosides:Aminoglycoside_efflux_pumps:KDPE	NA
contig00017	78082	78471	MARA	0/0	100.0	99.5	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00017	77633	78067	MARR	0/0	100.0	97.9	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00014	32376	33608	MDFA	0/0	100.0	98.2	MEG_3737	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDFA	NA
contig00026	20832	22079	MDTA	0/0	100.0	98.2	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00026	17710	20832	MDTB	0/0	100.0	98.0	MEG_3747	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTB	NA
contig00026	14632	17709	MDTC	0/0	100.0	98.1	MEG_3749	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTC	NA
contig00010	49568	50725	MDTE	0/0	100.0	98.8	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00010	50750	53863	MDTF	0/0	100.0	98.5	MEG_3752	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTF	NA
contig00005	44635	45861	MDTG	0/0	100.0	98.7	MEG_3753	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig00005	34796	36004	MDTH	0/0	100.0	97.8	MEG_3755	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTH	NA
contig00023	35467	35796	MDTI	0/0	100.0	99.7	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00023	35115	35480	MDTJ	0/0	100.0	98.1	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00003	280971	282343	MDTK	0/0	99.9	98.2	MEG_3759	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:MDTK	NA
contig00002	284727	285959	MDTM	0/0	100.0	96.5	MEG_3761	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTM	NA
contig00004	43659	44690	MDTN	0/0	100.0	96.4	MEG_3763	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN	NA
contig00004	41608	43659	MDTO	0/0	100.0	96.3	MEG_3764	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTO	NA
contig00004	40145	41611	MDTP	0/0	100.0	97.5	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig00011	113536	114010	MPHB	0/0	99.6	96.6	MEG_4033	Drugs:MLS:Macrolide_phosphotransferases:MPHB	NA
contig00005	179254	181002	MSBA	0/0	100.0	99.0	MEG_4061	Drugs:Multi-drug_resistance:Multi-drug_ABC_efflux_pumps:MSBA	NA
contig00080	220	1032	NDM	0/0	100.0	100.0	MEG_4147	Drugs:betalactams:Class_B_betalactamases:NDM	NA
contig00015	50396	52297	PBP2	0/0	100.0	99.0	MEG_5400	Drugs:betalactams:Penicillin_binding_protein:PBP2	NA
contig00001	401770	403074	PBP4B	0/0	100.0	96.0	MEG_5409	Drugs:betalactams:Penicillin_binding_protein:PBP4B	NA
contig00001	194864	195832	PMRF	0/0	100.0	98.1	MEG_5801	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF	NA
contig00057	5278	5934	QNRS	0/0	100.0	100.0	MEG_6020	Drugs:Fluoroquinolones:Quinolone_resistance_protein_Qnr:QNRS	NA
contig00002	233158	234027	ROBA	0/0	100.0	99.5	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00004	18179	18501	SOXS	0/0	99.7	97.5	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00070	2442	3257	SULII	0/0	100.0	100.0	MEG_6617	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULII	NA
contig00052	2881	4126	TEM	0/0	98.3	99.4	MEG_6875	Drugs:betalactams:Class_A_betalactamases:TEM	NA
contig00052	317	1591	TETA	0/0	100.0	100.0	MEG_7024	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETA	NA
contig00044	20936	22102	UGD	0/0	100.0	96.2	MEG_7328	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:UGD	NA
contig00001	131725	133368	YOGI	0/0	100.0	97.5	MEG_7842	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:YOGI	NA

ID178

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00058	1443	2231	aadA5_1	0/0	100	100.0	AF137361	aadA5	Streptomycin
contig00031	29159	29995	aph(6)-Id_1	0/0	100	100.0	M28829	aph(6)-Id	Streptomycin
contig00072	427	1302	blaCTX-M-27_1	0/0	100	100.0	AY156923	blaCTX-M-27	Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig00031	28327	28809	dfrA14_5	0/0	100	99.8	DQ388123	dfrA14	Trimethoprim
contig00058	839	1312	dfrA17_1	0/0	100	100.0	FJ460238	dfrA17	Trimethoprim
contig00079	266	1029	erm(B)_18	2/2	100	99.0	X66468	erm(B)	Erythromycin, Lincomycin, Clindamycin, Quinupristin, Pristinamycin_IA, Virginiamycin_S
contig00003	66772	68004	mdf(A)_1	0/0	100	98.3	Y08743	mdf(A)
contig00085	67	997	mph(A)_2	2/10	100	98.7	U36578	mph(A)	Erythromycin, Azithromycin, Spiramycin, Telithromycin
contig00058	2751	3617	sul1_5	0/0	100	99.9	EU780013	sul1	Sulfamethoxazole
contig00031	26912	27727	sul2_2	0/0	100	100.0	AY034138	sul2	Sulfamethoxazole
contig00067	1356	2561	tet(B)_2	0/0	100	100.0	AF326777	tet(B)	Doxycycline, Tetracycline, Minocycline

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00058	1443	2231	aadA5	0/0	100.0	100.0	AF137361:63-852	aadA5 is an aminoglycoside nucleotidyltransferase gene encoded by plasmids transposons and integrons in E. coli K. pneumoniae Kluyvera georgiana P. aeruginosa and E. cloacae	aminoglycoside
contig00006	89136	92285	acrB	0/0	100.0	99.0	U00096.3:484403-481253	Protein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug/proton antiporter.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00001	339529	342642	acrD	0/0	100.0	98.7	AP009048.1:2586250-2589364	AcrD is an aminoglycoside efflux pump expressed in E. coli. Its expression can be induced by indole and is regulated by baeRS and cpxAR.	aminoglycoside
contig00005	289450	290607	acrE	0/0	100.0	98.2	U00096:3413863-3415021	AcrE is a membrane fusion protein similar to AcrA.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00005	290619	293723	acrF	0/0	100.0	97.5	U00096:3415032-3418137	AcrF is a inner membrane transporter similar to AcrB.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00005	288389	289051	acrS	0/0	100.0	97.6	U00096:3413465-3412802	AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.	cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00031	29159	29995	APH(6)-Id	0/0	100.0	99.9	AF024602:3155-3992	APH(6)-Id is an aminoglycoside phosphotransferase encoded by plasmids integrative conjugative elements and chromosomal genomic islands in K. pneumoniae Salmonella spp. E. coli Shigella flexneri Providencia alcalifaciens Pseudomonas spp. V. cholerae Edwardsiella tarda Pasteurella multocida and Aeromonas bestiarum	aminoglycoside
contig00005	75623	76442	bacA	0/0	99.8	97.0	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00014	63311	64032	baeR	0/0	99.9	97.0	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00014	64029	65432	baeS	0/0	100.0	92.2	AP009048:2165012-2166416	BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.	aminocoumarin, aminoglycoside
contig00017	22665	24038	cpxA	0/0	100.0	98.9	BA000007.3:4905062-4903688	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	aminocoumarin, aminoglycoside
contig00008	15337	15969	CRP	0/0	100.0	99.2	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00072	427	1302	CTX-M-27	0/0	100.0	100.0	AY156923:0-876	CTX-M-27 is a beta-lactamase found in Escherichia coli	cephalosporin
contig00031	28327	28809	dfrA14	0/0	100.0	100.0	EU780012:2162-2645	dfrA14 is an integron-encoded dihydrofolate reductase found in Escherichia coli	diaminopyrimidine
contig00058	839	1312	dfrA17	0/0	100.0	100.0	DQ838665:0-474	dfrA17 is an integron-encoded dihydrofolate reductase found in Escherichia coli	diaminopyrimidine
contig00013	55312	56484	emrA	0/0	100.0	98.1	AP009048:2810082-2811255	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	fluoroquinolone
contig00013	56501	58039	emrB	0/0	100.0	98.5	U00096:2812615-2814154	emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin.	fluoroquinolone
contig00001	241672	242727	emrK	0/0	100.0	96.9	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00013	54655	55185	emrR	0/0	100.0	99.4	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00001	240134	241672	emrY	0/0	100.0	98.0	D78168:1591-3130	emrY is a multidrug transport that moves substrates across the inner membrane of the Gram-negative E. coli. It is a homolog of emrB.	tetracycline
contig00009	175498	177141	eptA	0/0	100.0	98.2	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00079	292	1037	ErmB	1/1	99.9	99.2	AF242872.1:2131-2878	ErmB confers the MLSb phenotype. Similar to ErmC expression of ErmB is inducible by erythromycin. The leader peptide causes attenuation of the mRNA and stabilizes the structure preventing further translation. When erythromycin is present it binds the leader peptide causing a change in conformation allowing for the expression of ErmB.	lincosamide, macrolide, streptogramin
contig00006	87920	89113	Escherichia_coli_acrA	0/0	100.0	99.0	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00011	134704	135837	Escherichia_coli_ampC	0/0	100.0	98.1	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00001	304996	306300	Escherichia_coli_ampC1_beta-lactamase	0/0	100.0	95.2	FN649414.1:2765050-2766355	An ampC-like beta-lactamase identified from Escherichia coli.	cephalosporin, penam
contig00006	178534	179691	Escherichia_coli_ampH	0/0	100.0	97.3	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig00006	3833	4165	Escherichia_coli_emrE	0/0	100.0	99.4	Z11877.1:485-818	Member of the small MDR (multidrug resistance) family of transporters, in Escherichia coli this protein provides resistance against a number of positively charged compounds including ethidium bromide and erythromycin, proton-dependent secondary transporter which exchanges protons for compound translocation	macrolide
contig00003	66772	68004	Escherichia_coli_mdfA	0/0	100.0	96.8	JQ394987:0-1233	Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter.	benzalkonium_chloride, rhodamine, tetracycline
contig00001	243250	243864	evgA	0/0	100.0	99.3	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00001	243869	247462	evgS	0/0	100.0	96.6	U00096:2484373-2487967	EvgS is a sensor protein that phosphorylates the regulatory protein EvgA. evgS corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	fluoroquinolone, macrolide, penam, tetracycline
contig00008	194552	195280	gadW	0/0	100.0	95.9	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig00008	195649	196473	gadX	0/0	100.0	93.9	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00027	1492	1905	H-NS	0/0	100.0	99.5	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00003	245281	245958	kdpE	0/0	100.0	95.6	U00096.3:721733-721055	kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding.	aminoglycoside
contig00028	27851	28234	marA	0/0	100.0	100.0	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00014	73045	74292	mdtA	0/0	100.0	96.5	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00014	69923	73045	mdtB	0/0	100.0	96.9	U00096:2155262-2158385	MdtB is a transporter that forms a heteromultimer complex with MdtC to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex.	aminocoumarin
contig00014	66845	69922	mdtC	0/0	100.0	96.7	U00096:2158385-2161463	MdtC is a transporter that forms a heteromultimer complex with MdtB to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex. In the absence of MdtB MdtC can form a homomultimer complex that results in a functioning efflux complex with a narrower drug specificity. mdtC corresponds to 3 loci in Pseudomonas aeruginosa PAO1 (gene name: muxC/muxB) and 3 loci in Pseudomonas aeruginosa LESB58.	aminocoumarin
contig00008	189894	191051	mdtE	0/0	100.0	99.0	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00008	191076	194189	mdtF	0/0	100.0	98.4	U00096:3660413-3663527	MdtF is the multidrug inner membrane transporter for the MdtEF-TolC efflux complex.	fluoroquinolone, macrolide, penam
contig00007	186100	187326	mdtG	0/0	100.0	98.3	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00007	195957	197165	mdtH	0/0	100.0	98.0	U00096:1125326-1124117	Multidrug resistance protein MdtH	fluoroquinolone
contig00004	287427	288638	mdtM	0/0	98.3	95.5	U00096.3:4568519-4567286	Multidrug resistance protein MdtM	acridine_dye, fluoroquinolone, lincosamide, nucleoside, phenicol
contig00009	145286	146317	mdtN	0/0	100.0	97.7	AP009048.1:4307588-4306556	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	acridine_dye, nucleoside
contig00009	143235	145286	mdtO	0/0	100.0	96.6	AP009048.1:4306557-4304505	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00009	141772	143238	mdtP	0/0	100.0	96.5	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00085	67	969	mphA	0/0	99.7	100.0	D16251.1:2531-1625	The mphA gene encodes for resistance enzyme MPH(2’)-I which preferentially inactivate 14-membered macrolides (e.g.erythromycin telithromycin roxithromycin) over 16-membered macrolides (e.g.tylosin spiramycin). It phosphorylates macrolides at 2’-OH hydroxyl of desosamine sugar of macrolides in a GTP-dependent manner.	macrolide
contig00001	363349	363823	mphB	0/0	99.6	96.2	AE005174.2:3397370-3397847	The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides.	macrolide
contig00007	51564	53312	msbA	0/0	100.0	98.9	U00096.3:966620-968369	MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability.	nitroimidazole
contig00001	137292	138260	pmrF	0/0	100.0	97.9	U00096:2367070-2368039	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide
contig00058	2778	3617	sul1	0/0	100.0	100.0	JF969163:1053-1893	Sul1 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria. It is linked to other resistance genes of class 1 integrons.	sulfonamide
contig00031	26912	27727	sul2	0/0	100.0	100.0	AY055428.1:21084-20268	Sul2 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria usually found on small plasmids.	sulfonamide
contig00067	1356	2561	tet(B)	0/0	100.0	99.8	AB089595:0-1206	Tet(B) is a tetracycline efflux protein expressed in many Gram-negative bacteria. It confers resistance to tetracycline doxycycline and minocycline but not tigecycline.	tetracycline
contig00005	53808	55295	tolC	0/0	100.0	97.9	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan
contig00034	4269	5435	ugd	0/0	100.0	97.3	U00096:2099613-2098446	PmrE is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin	peptide
contig00001	75471	77114	yojI	0/0	100.0	97.8	U00096.3:2308615-2306971	YojI mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. YojI is capable of pumping out microcin molecules. The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI.	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00058	1443	2231	(AGly)aadA5	0/0	100.0	100.0	AF137361:64-852	(AGly)aadA5	NA
contig00031	29159	29995	(AGly)strB	0/0	100.0	100.0	FJ474091:264-1100	(AGly)strB	NA
contig00001	304996	306300	(Bla)AmpC1_Ecoli	0/0	100.0	95.2	FN649414:2765051-2766355	(Bla)AmpC1_Ecoli	NA
contig00011	134704	135837	(Bla)AmpC2_Ecoli	0/0	100.0	98.1	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00006	178534	179691	(Bla)ampH_Ecoli	0/0	100.0	97.3	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00072	427	1302	(Bla)blaCTX-M-27	0/0	100.0	100.0	AY156923:1-876	(Bla)blaCTX-M-27	NA
contig00003	299814	301715	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100.0	98.4	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA
contig00079	292	1029	(MLS)erm(B)	0/0	100.0	99.6	M11180:714-1451	(MLS)erm(B)	NA
contig00085	67	969	(MLS)mph(A)	0/0	99.7	100.0	DQ445270:1626-2531	(MLS)mph(A)	NA
contig00058	2778	3617	(Sul)sul1	0/0	100.0	100.0	AF071413:6700-7539	(Sul)sul1	NA
contig00031	26912	27727	(Sul)sul2	0/0	100.0	100.0	EU360945:1617-2432	(Sul)sul2	NA
contig00067	1356	2561	(Tet)tetB	0/0	100.0	99.7	AB089594:1-1206	(Tet)tetB	NA
contig00031	28336	28809	(Tmt)dfrA14	0/0	100.0	99.8	GU726917:72-545	(Tmt)dfrA14	NA
contig00058	839	1312	(Tmt)dfrA17	0/0	100.0	100.0	AB126604:98-571	(Tmt)dfrA17	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00058	1443	2231	aadA5	0/0	100	100.0	NG_047357.1	ANT(3’’)-Ia family aminoglycoside nucleotidyltransferase AadA5	STREPTOMYCIN
contig00031	29159	29995	aph(6)-Id	0/0	100	100.0	NG_047464.1	aminoglycoside O-phosphotransferase APH(6)-Id	STREPTOMYCIN
contig00072	427	1302	blaCTX-M-27	0/0	100	100.0	NG_048976.1	class A extended-spectrum beta-lactamase CTX-M-27	CEPHALOSPORIN
contig00011	134704	135837	blaEC-19	0/0	100	99.9	NG_049084.1	class C extended-spectrum beta-lactamase EC-19	CEPHALOSPORIN
contig00031	28336	28809	dfrA14	0/0	100	100.0	NG_047696.1	trimethoprim-resistant dihydrofolate reductase DfrA14	TRIMETHOPRIM
contig00058	839	1312	dfrA17	0/0	100	99.8	NG_047710.1	trimethoprim-resistant dihydrofolate reductase DfrA17	TRIMETHOPRIM
contig00079	292	1029	erm(B)	0/0	100	99.9	NG_047804.1	23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(B)	MACROLIDE
contig00085	67	997	mph(A)	2/10	100	98.7	NG_047986.1	Mph(A) family macrolide 2’-phosphotransferase	MACROLIDE
contig00058	2778	3617	sul1	0/0	100	100.0	NG_048082.1	sulfonamide-resistant dihydropteroate synthase Sul1	SULFONAMIDE
contig00031	26912	27727	sul2	0/0	100	100.0	NG_051852.1	sulfonamide-resistant dihydropteroate synthase Sul2	SULFONAMIDE
contig00067	1356	2561	tet(B)	0/0	100	100.0	NG_048163.1	tetracycline efflux MFS transporter Tet(B)	TETRACYCLINE

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00006	87920	89113	ACRA	0/0	100.0	99.0	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00006	89136	92285	ACRB	0/0	100.0	99.0	MEG_401	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRB	NA
contig00001	339529	342642	ACRD	0/0	100.0	98.7	MEG_407	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ACRD	NA
contig00005	289450	290607	ACRE	0/0	100.0	98.2	MEG_408	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRE	NA
contig00005	290619	293723	ACRF	0/0	100.0	97.5	MEG_409	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRF	NA
contig00005	288389	289051	ACRS	0/0	100.0	97.6	MEG_415	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS	NA
contig00006	178534	179691	AMPH	0/0	100.0	97.3	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00058	1443	2231	ANT3-DPRIME	0/0	100.0	100.0	MEG_928	Drugs:Aminoglycosides:Aminoglycoside_O-nucleotidyltransferases:ANT3-DPRIME	NA
contig00031	29159	29995	APH6	0/0	100.0	100.0	MEG_1086	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH6	NA
contig00014	85900	87753	ASMA	0/0	100.0	97.8	MEG_1180	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:ASMA	NA
contig00005	75623	76442	BACA	0/0	99.8	97.2	MEG_1189	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00014	63311	64032	BAER	0/0	99.9	97.0	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00014	64029	65432	BAES	0/0	100.0	92.2	MEG_1193	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES	NA
contig00001	49008	50198	BCR	0/0	100.0	96.6	MEG_1210	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR	NA
contig00011	134704	135837	BLAEC	0/0	100.0	99.9	MEG_1277	Drugs:betalactams:Class_C_betalactamases:BLAEC	NA
contig00017	21970	22668	CPXAR	0/0	100.0	99.4	MEG_2118	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00017	22665	24038	CPXAR	0/0	100.0	99.0	MEG_2121	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00008	15337	15969	CRP	0/0	100.0	99.2	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00072	405	1308	CTX	0/0	100.0	99.8	MEG_2401	Drugs:betalactams:Class_A_betalactamases:CTX	NA
contig00072	1337	2279	CTX	0/0	100.0	100.0	MEG_2435	Drugs:betalactams:Class_A_betalactamases:CTX	NA
contig00031	28336	28809	DFRA	0/0	100.0	100.0	MEG_2517	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00058	839	1312	DFRA	0/0	100.0	100.0	MEG_2547	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00013	55312	56484	EMRA	0/0	100.0	98.1	MEG_2722	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA	NA
contig00013	56501	58039	EMRB	0/0	100.0	98.5	MEG_2725	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRB	NA
contig00015	89688	90878	EMRD	0/0	100.0	97.8	MEG_2729	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD	NA
contig00001	241672	242835	EMRK	0/0	100.0	96.7	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig00013	54655	55185	EMRR	0/0	100.0	99.4	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00001	240134	241672	EMRY	0/0	100.0	98.1	MEG_2736	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRY	NA
contig00009	175498	177141	EPTA	0/0	100.0	98.2	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig00079	266	1029	ERMB	2/2	100.0	99.0	MEG_2801	Drugs:MLS:23S_rRNA_methyltransferases:ERMB	NA
contig00001	243869	247462	EVGS	0/0	100.0	97.1	MEG_2869	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EVGS	NA
contig00008	194552	195280	GADW	0/0	100.0	97.0	MEG_3081	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig00008	195649	196473	GADX	0/0	100.0	93.9	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00027	1492	1905	HNS	0/0	100.0	99.5	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00003	245281	245958	KDPE	0/0	100.0	95.6	MEG_3448	Drugs:Aminoglycosides:Aminoglycoside_efflux_pumps:KDPE	NA
contig00028	27845	28234	MARA	0/0	100.0	100.0	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00028	27396	27830	MARR	0/0	100.0	98.6	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00003	66772	68004	MDFA	0/0	100.0	98.4	MEG_3737	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDFA	NA
contig00014	73045	74292	MDTA	0/0	100.0	96.5	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00014	69923	73045	MDTB	0/0	100.0	96.9	MEG_3747	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTB	NA
contig00014	66845	69922	MDTC	0/0	100.0	96.7	MEG_3749	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTC	NA
contig00008	189894	191051	MDTE	0/0	100.0	99.0	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00008	191076	194189	MDTF	0/0	100.0	98.4	MEG_3752	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTF	NA
contig00007	186100	187326	MDTG	0/0	100.0	98.7	MEG_3753	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig00007	195957	197165	MDTH	0/0	100.0	98.0	MEG_3755	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTH	NA
contig00002	326152	326481	MDTI	0/0	100.0	99.7	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00002	325800	326165	MDTJ	0/0	100.0	98.6	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00002	258799	260171	MDTK	0/0	99.9	97.9	MEG_3759	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:MDTK	NA
contig00004	287427	288638	MDTM	0/0	98.3	95.5	MEG_3761	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTM	NA
contig00009	145286	146317	MDTN	0/0	100.0	97.7	MEG_3763	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN	NA
contig00009	143235	145286	MDTO	0/0	100.0	96.6	MEG_3764	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTO	NA
contig00009	141772	143238	MDTP	0/0	100.0	96.5	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig00085	67	997	MPHA	2/10	100.0	98.7	MEG_4030	Drugs:MLS:Macrolide_phosphotransferases:MPHA	NA
contig00001	363349	363823	MPHB	0/0	99.6	96.2	MEG_4033	Drugs:MLS:Macrolide_phosphotransferases:MPHB	NA
contig00007	51564	53312	MSBA	0/0	100.0	98.9	MEG_4061	Drugs:Multi-drug_resistance:Multi-drug_ABC_efflux_pumps:MSBA	NA
contig00006	3833	4165	MVRC	0/0	100.0	99.4	MEG_4103	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MVRC	NA
contig00003	299814	301715	PBP2	0/0	100.0	98.4	MEG_5400	Drugs:betalactams:Penicillin_binding_protein:PBP2	NA
contig00001	304996	306300	PBP4B	0/0	100.0	95.2	MEG_5409	Drugs:betalactams:Penicillin_binding_protein:PBP4B	NA
contig00001	137292	138260	PMRF	0/0	100.0	97.9	MEG_5801	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF	NA
contig00004	238073	238942	ROBA	0/0	100.0	99.0	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00009	121249	121571	SOXS	0/0	99.7	97.8	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00058	2777	3744	SULI	0/0	100.0	100.0	MEG_6615	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULI	NA
contig00031	26912	27727	SULII	0/0	100.0	100.0	MEG_6617	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULII	NA
contig00067	1356	2561	TETB	0/0	100.0	100.0	MEG_7052	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETB	NA
contig00034	4269	5435	UGD	0/0	100.0	97.3	MEG_7328	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:UGD	NA
contig00001	75471	77114	YOGI	0/0	100.0	97.8	MEG_7842	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:YOGI	NA

ID182

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00083	323	1159	aph(6)-Id_1	0/0	100	100.0	M28829	aph(6)-Id	Streptomycin
contig00003	91983	92858	blaCTX-M-55_1	0/0	100	100.0	DQ810789	blaCTX-M-55	Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig00083	1509	1991	dfrA14_5	0/0	100	99.8	DQ388123	dfrA14	Trimethoprim
contig00012	30613	31845	mdf(A)_1	0/0	100	98.8	Y08743	mdf(A)
contig00083	2591	3406	sul2_2	0/0	100	100.0	AY034138	sul2	Sulfamethoxazole
contig00083	6757	8031	tet(A)_6	0/0	100	100.0	AF534183	tet(A)	Doxycycline, Tetracycline

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00006	39451	42600	acrB	0/0	100.0	100.0	U00096.3:484403-481253	Protein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug/proton antiporter.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00022	38195	41308	acrD	0/0	100.0	99.7	AP009048.1:2586250-2589364	AcrD is an aminoglycoside efflux pump expressed in E. coli. Its expression can be induced by indole and is regulated by baeRS and cpxAR.	aminoglycoside
contig00033	4929	6086	acrE	0/0	100.0	98.9	U00096:3413863-3415021	AcrE is a membrane fusion protein similar to AcrA.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00033	1813	4917	acrF	0/0	100.0	99.2	U00096:3415032-3418137	AcrF is a inner membrane transporter similar to AcrB.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00033	6485	7147	acrS	0/0	100.0	98.9	U00096:3413465-3412802	AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.	cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00083	323	1159	APH(6)-Id	0/0	100.0	99.9	AF024602:3155-3992	APH(6)-Id is an aminoglycoside phosphotransferase encoded by plasmids integrative conjugative elements and chromosomal genomic islands in K. pneumoniae Salmonella spp. E. coli Shigella flexneri Providencia alcalifaciens Pseudomonas spp. V. cholerae Edwardsiella tarda Pasteurella multocida and Aeromonas bestiarum	aminoglycoside
contig00021	65667	66488	bacA	0/0	100.0	99.5	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00004	97198	97920	baeR	0/0	100.0	100.0	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00004	95798	97201	baeS	0/0	100.0	100.0	AP009048:2165012-2166416	BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.	aminocoumarin, aminoglycoside
contig00015	61258	62631	cpxA	0/0	100.0	98.9	BA000007.3:4905062-4903688	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	aminocoumarin, aminoglycoside
contig00013	14935	15567	CRP	0/0	100.0	99.8	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00003	91983	92858	CTX-M-55	0/0	100.0	100.0	DQ885477:0-876	CTX-M-55 is a beta-lactamase found in the Enterobacteriaceae family	cephalosporin
contig00083	1509	1991	dfrA14	0/0	100.0	100.0	EU780012:2162-2645	dfrA14 is an integron-encoded dihydrofolate reductase found in Escherichia coli	diaminopyrimidine
contig00011	25850	27022	emrA	0/0	100.0	100.0	AP009048:2810082-2811255	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	fluoroquinolone
contig00011	27039	28577	emrB	0/0	100.0	100.0	U00096:2812615-2814154	emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin.	fluoroquinolone
contig00029	5169	6224	emrK	0/0	100.0	99.8	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00011	25193	25723	emrR	0/0	100.0	100.0	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00029	3631	5169	emrY	0/0	100.0	99.0	D78168:1591-3130	emrY is a multidrug transport that moves substrates across the inner membrane of the Gram-negative E. coli. It is a homolog of emrB.	tetracycline
contig00039	7712	9355	eptA	0/0	100.0	100.0	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00006	38235	39428	Escherichia_coli_acrA	0/0	100.0	100.0	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00036	31253	32386	Escherichia_coli_ampC	0/0	100.0	97.3	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00054	10718	12022	Escherichia_coli_ampC1_beta-lactamase	0/0	100.0	100.0	FN649414.1:2765050-2766355	An ampC-like beta-lactamase identified from Escherichia coli.	cephalosporin, penam
contig00006	127461	128618	Escherichia_coli_ampH	0/0	100.0	99.0	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig00012	30613	31845	Escherichia_coli_mdfA	0/0	100.0	97.2	JQ394987:0-1233	Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter.	benzalkonium_chloride, rhodamine, tetracycline
contig00029	6748	7362	evgA	0/0	100.0	99.8	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00029	7367	10960	evgS	0/0	100.0	99.7	U00096:2484373-2487967	EvgS is a sensor protein that phosphorylates the regulatory protein EvgA. evgS corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	fluoroquinolone, macrolide, penam, tetracycline
contig00047	2613	3341	gadW	0/0	100.0	94.7	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig00047	1421	2245	gadX	0/0	100.0	99.8	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00009	62464	62877	H-NS	0/0	100.0	99.5	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00008	5503	6180	kdpE	0/0	100.0	99.8	U00096.3:721733-721055	kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding.	aminoglycoside
contig00035	29821	30204	marA	0/0	100.0	99.7	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00004	86938	88185	mdtA	0/0	100.0	92.8	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00004	88185	91307	mdtB	0/0	100.0	94.0	U00096:2155262-2158385	MdtB is a transporter that forms a heteromultimer complex with MdtC to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex.	aminocoumarin
contig00004	91308	94385	mdtC	0/0	100.0	99.8	U00096:2158385-2161463	MdtC is a transporter that forms a heteromultimer complex with MdtB to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex. In the absence of MdtB MdtC can form a homomultimer complex that results in a functioning efflux complex with a narrower drug specificity. mdtC corresponds to 3 loci in Pseudomonas aeruginosa PAO1 (gene name: muxC/muxB) and 3 loci in Pseudomonas aeruginosa LESB58.	aminocoumarin
contig00047	6842	7999	mdtE	0/0	100.0	100.0	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00047	3704	6817	mdtF	0/0	100.0	99.9	U00096:3660413-3663527	MdtF is the multidrug inner membrane transporter for the MdtEF-TolC efflux complex.	fluoroquinolone, macrolide, penam
contig00014	82588	83814	mdtG	0/0	100.0	99.3	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00014	72749	73957	mdtH	0/0	100.0	97.8	U00096:1125326-1124117	Multidrug resistance protein MdtH	fluoroquinolone
contig00010	69982	71193	mdtM	0/0	98.3	95.9	U00096.3:4568519-4567286	Multidrug resistance protein MdtM	acridine_dye, fluoroquinolone, lincosamide, nucleoside, phenicol
contig00053	27191	28222	mdtN	0/0	100.0	99.9	AP009048.1:4307588-4306556	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	acridine_dye, nucleoside
contig00053	25140	27191	mdtO	0/0	100.0	100.0	AP009048.1:4306557-4304505	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00053	23677	25143	mdtP	0/0	100.0	99.9	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00022	17041	17517	mphB	0/0	100.0	98.3	AE005174.2:3397370-3397847	The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides.	macrolide
contig00016	51216	52964	msbA	0/0	100.0	100.0	U00096.3:966620-968369	MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability.	nitroimidazole
contig00026	14612	15580	pmrF	0/0	100.0	98.2	U00096:2367070-2368039	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide
contig00083	2591	3406	sul2	0/0	100.0	100.0	AY055428.1:21084-20268	Sul2 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria usually found on small plasmids.	sulfonamide
contig00083	6757	8031	tet(A)	0/0	100.0	100.0	AF534183.1:2970-4245	TetA is a tetracycline efflux pump found in many species of Gram-negative bacteria.	tetracycline
contig00021	41802	43289	tolC	0/0	100.0	99.7	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan
contig00004	48832	49998	ugd	0/0	100.0	96.7	U00096:2099613-2098446	PmrE is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin	peptide
contig00085	4400	6043	yojI	0/0	100.0	98.3	U00096.3:2308615-2306971	YojI mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. YojI is capable of pumping out microcin molecules. The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI.	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00083	323	1159	(AGly)strB	0/0	100.0	100.0	FJ474091:264-1100	(AGly)strB	NA
contig00054	10718	12022	(Bla)AmpC1_Ecoli	0/0	100.0	100.0	FN649414:2765051-2766355	(Bla)AmpC1_Ecoli	NA
contig00036	31253	32386	(Bla)AmpC2_Ecoli	0/0	100.0	97.3	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00006	127461	128618	(Bla)ampH_Ecoli	0/0	100.0	99.0	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00003	91983	92858	(Bla)blaCTX-M-55	0/0	100.0	100.0	HM748991:321-1196	(Bla)blaCTX-M-55	NA
contig00008	57889	59790	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100.0	99.0	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA
contig00083	2591	3406	(Sul)sul2	0/0	100.0	100.0	EU360945:1617-2432	(Sul)sul2	NA
contig00083	6785	8031	(Tet)tetA	0/0	97.8	100.0	JX424423:94438-95712	(Tet)tetA	NA
contig00083	8062	8712	(Tet)tetR	0/0	100.0	99.8	HF545434:53576-54226	(Tet)tetR	NA
contig00083	1509	1982	(Tmt)dfrA14	0/0	100.0	99.8	GU726917:72-545	(Tmt)dfrA14	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00083	323	1159	aph(6)-Id	0/0	100	100.0	NG_047464.1	aminoglycoside O-phosphotransferase APH(6)-Id	STREPTOMYCIN
contig00003	91983	92858	blaCTX-M-55	0/0	100	100.0	NG_049006.1	class A extended-spectrum beta-lactamase CTX-M-55	CEPHALOSPORIN
contig00036	31253	32386	blaEC-15	0/0	100	98.6	NG_049081.1	class C extended-spectrum beta-lactamase EC-15	CEPHALOSPORIN
contig00083	1509	1982	dfrA14	0/0	100	100.0	NG_047696.1	trimethoprim-resistant dihydrofolate reductase DfrA14	TRIMETHOPRIM
contig00083	2591	3406	sul2	0/0	100	100.0	NG_051852.1	sulfonamide-resistant dihydropteroate synthase Sul2	SULFONAMIDE
contig00083	6757	7956	tet(A)	0/0	100	100.0	NG_048153.1	tetracycline efflux MFS transporter Tet(A)	TETRACYCLINE

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00006	38235	39428	ACRA	0/0	100.0	100.0	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00006	39451	42600	ACRB	0/0	100.0	100.0	MEG_401	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRB	NA
contig00022	38195	41308	ACRD	0/0	100.0	99.7	MEG_407	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ACRD	NA
contig00033	4929	6086	ACRE	0/0	100.0	98.9	MEG_408	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRE	NA
contig00033	1813	4917	ACRF	0/0	100.0	99.2	MEG_409	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRF	NA
contig00033	6485	7147	ACRS	0/0	100.0	98.9	MEG_415	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS	NA
contig00006	127461	128618	AMPH	0/0	100.0	99.0	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00083	323	1159	APH6	0/0	100.0	100.0	MEG_1086	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH6	NA
contig00021	65667	66488	BACA	0/0	100.0	99.5	MEG_1189	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00004	97198	97920	BAER	0/0	100.0	100.0	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00004	95798	97201	BAES	0/0	100.0	100.0	MEG_1193	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES	NA
contig00020	49257	50447	BCR	0/0	100.0	99.9	MEG_1210	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR	NA
contig00036	31253	32386	BLAEC	0/0	100.0	98.6	MEG_1282	Drugs:betalactams:Class_C_betalactamases:BLAEC	NA
contig00015	60563	61261	CPXAR	0/0	100.0	99.9	MEG_2118	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00015	61258	62631	CPXAR	0/0	100.0	99.8	MEG_2121	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00013	14935	15567	CRP	0/0	100.0	99.8	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00083	1509	1982	DFRA	0/0	100.0	100.0	MEG_2517	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00011	25850	27022	EMRA	0/0	100.0	100.0	MEG_2722	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA	NA
contig00011	27039	28577	EMRB	0/0	100.0	100.0	MEG_2725	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRB	NA
contig00025	17886	19076	EMRD	0/0	100.0	100.0	MEG_2729	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD	NA
contig00029	5169	6332	EMRK	0/0	100.0	99.8	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig00011	25193	25723	EMRR	0/0	100.0	100.0	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00029	3631	5169	EMRY	0/0	100.0	99.1	MEG_2736	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRY	NA
contig00039	7712	9355	EPTA	0/0	100.0	100.0	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig00029	7367	10960	EVGS	0/0	100.0	99.7	MEG_2870	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EVGS	NA
contig00047	2613	3341	GADW	0/0	100.0	100.0	MEG_3081	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig00047	1421	2245	GADX	0/0	100.0	99.8	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00009	62464	62877	HNS	0/0	100.0	99.5	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00008	5503	6180	KDPE	0/0	100.0	99.8	MEG_3448	Drugs:Aminoglycosides:Aminoglycoside_efflux_pumps:KDPE	NA
contig00035	29815	30204	MARA	0/0	100.0	99.7	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00035	29367	29801	MARR	0/0	100.0	97.9	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00012	30613	31845	MDFA	0/0	100.0	98.9	MEG_3737	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDFA	NA
contig00004	86938	88185	MDTA	0/0	100.0	92.8	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00004	88185	91307	MDTB	0/0	100.0	94.0	MEG_3747	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTB	NA
contig00004	91308	94385	MDTC	0/0	100.0	99.8	MEG_3749	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTC	NA
contig00047	6842	7999	MDTE	0/0	100.0	100.0	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00047	3704	6817	MDTF	0/0	100.0	99.9	MEG_3752	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTF	NA
contig00014	82588	83814	MDTG	0/0	100.0	99.9	MEG_3753	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig00014	72749	73957	MDTH	0/0	100.0	97.8	MEG_3755	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTH	NA
contig00061	19868	20197	MDTI	0/0	100.0	99.7	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00061	20184	20549	MDTJ	0/0	100.0	99.2	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00019	30650	32023	MDTK	0/0	100.0	100.0	MEG_3759	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:MDTK	NA
contig00010	69982	71193	MDTM	0/0	98.3	95.9	MEG_3761	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTM	NA
contig00053	27191	28222	MDTN	0/0	100.0	99.9	MEG_3763	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN	NA
contig00053	25140	27191	MDTO	0/0	100.0	100.0	MEG_3764	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTO	NA
contig00053	23677	25143	MDTP	0/0	100.0	99.9	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig00022	17041	17517	MPHB	0/0	100.0	98.3	MEG_4033	Drugs:MLS:Macrolide_phosphotransferases:MPHB	NA
contig00016	51216	52964	MSBA	0/0	100.0	100.0	MEG_4061	Drugs:Multi-drug_resistance:Multi-drug_ABC_efflux_pumps:MSBA	NA
contig00008	57889	59790	PBP2	0/0	100.0	99.0	MEG_5400	Drugs:betalactams:Penicillin_binding_protein:PBP2	NA
contig00054	10718	12022	PBP4B	0/0	100.0	100.0	MEG_5409	Drugs:betalactams:Penicillin_binding_protein:PBP4B	NA
contig00026	14612	15580	PMRF	0/0	100.0	98.2	MEG_5801	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF	NA
contig00010	21727	22596	ROBA	0/0	100.0	98.8	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00053	1285	1607	SOXS	0/0	99.7	99.7	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00083	2591	3406	SULII	0/0	100.0	100.0	MEG_6617	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULII	NA
contig00083	6757	8031	TETA	0/0	100.0	100.0	MEG_7025	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETA	NA
contig00004	48832	49998	UGD	0/0	100.0	96.7	MEG_7328	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:UGD	NA
contig00085	4400	6043	YOGI	0/0	100.0	98.3	MEG_7842	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:YOGI	NA

ID186

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00002	231391	232266	blaCTX-M-15_1	0/0	100	100.0	AY044436	blaCTX-M-15	Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig00024	26130	27362	mdf(A)_1	0/0	100	99.1	Y08743	mdf(A)
contig00002	226094	226750	qnrS1_1	0/0	100	100.0	AB187515	qnrS1	Ciprofloxacin

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00010	124682	127831	acrB	0/0	100.0	99.1	U00096.3:484403-481253	Protein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug/proton antiporter.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00006	117709	120822	acrD	0/0	100.0	98.8	AP009048.1:2586250-2589364	AcrD is an aminoglycoside efflux pump expressed in E. coli. Its expression can be induced by indole and is regulated by baeRS and cpxAR.	aminoglycoside
contig00004	270325	271482	acrE	0/0	100.0	99.0	U00096:3413863-3415021	AcrE is a membrane fusion protein similar to AcrA.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00004	271494	274598	acrF	0/0	100.0	99.0	U00096:3415032-3418137	AcrF is a inner membrane transporter similar to AcrB.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00004	269264	269926	acrS	0/0	100.0	98.6	U00096:3413465-3412802	AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.	cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00004	60021	60840	bacA	0/0	99.8	98.7	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00002	277506	278228	baeR	0/0	100.0	99.5	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00002	278225	279628	baeS	0/0	100.0	98.7	AP009048:2165012-2166416	BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.	aminocoumarin, aminoglycoside
contig00027	22569	23942	cpxA	0/0	100.0	98.5	BA000007.3:4905062-4903688	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	aminocoumarin, aminoglycoside
contig00037	15000	15632	CRP	0/0	100.0	99.2	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00002	231391	232266	CTX-M-15	0/0	100.0	100.0	AY044436:1435-2311	CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family	cephalosporin
contig00001	27204	28376	emrA	0/0	100.0	98.2	AP009048:2810082-2811255	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	fluoroquinolone
contig00001	28393	29931	emrB	0/0	100.0	98.5	U00096:2812615-2814154	emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin.	fluoroquinolone
contig00006	25955	27010	emrK	0/0	100.0	98.7	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00001	26547	27077	emrR	0/0	100.0	100.0	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00006	24417	25955	emrY	0/0	100.0	98.8	D78168:1591-3130	emrY is a multidrug transport that moves substrates across the inner membrane of the Gram-negative E. coli. It is a homolog of emrB.	tetracycline
contig00013	115182	116825	eptA	0/0	100.0	99.2	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00010	127854	129047	Escherichia_coli_acrA	0/0	100.0	99.8	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00023	50362	51495	Escherichia_coli_ampC	0/0	100.0	97.2	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00006	85287	86591	Escherichia_coli_ampC1_beta-lactamase	0/0	100.0	98.2	FN649414.1:2765050-2766355	An ampC-like beta-lactamase identified from Escherichia coli.	cephalosporin, penam
contig00010	36338	37495	Escherichia_coli_ampH	0/0	100.0	98.7	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig00008	136225	136557	Escherichia_coli_emrE	0/0	100.0	92.2	Z11877.1:485-818	Member of the small MDR (multidrug resistance) family of transporters, in Escherichia coli this protein provides resistance against a number of positively charged compounds including ethidium bromide and erythromycin, proton-dependent secondary transporter which exchanges protons for compound translocation	macrolide
contig00024	26130	27362	Escherichia_coli_mdfA	0/0	100.0	97.6	JQ394987:0-1233	Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter.	benzalkonium_chloride, rhodamine, tetracycline
contig00006	27534	28148	evgA	0/0	100.0	99.0	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00006	28153	31746	evgS	0/0	100.0	99.5	U00096:2484373-2487967	EvgS is a sensor protein that phosphorylates the regulatory protein EvgA. evgS corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	fluoroquinolone, macrolide, penam, tetracycline
contig00012	156374	157102	gadW	0/0	100.0	94.4	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig00012	157470	158294	gadX	0/0	100.0	97.8	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00005	158443	158856	H-NS	0/0	100.0	99.3	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00007	8327	8999	kdpE	0/0	99.3	97.2	U00096.3:721733-721055	kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding.	aminoglycoside
contig00017	29294	29677	marA	0/0	100.0	99.5	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00002	287241	288488	mdtA	0/0	100.0	98.2	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00002	284119	287241	mdtB	0/0	100.0	98.0	U00096:2155262-2158385	MdtB is a transporter that forms a heteromultimer complex with MdtC to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex.	aminocoumarin
contig00002	281041	284118	mdtC	0/0	100.0	98.1	U00096:2158385-2161463	MdtC is a transporter that forms a heteromultimer complex with MdtB to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex. In the absence of MdtB MdtC can form a homomultimer complex that results in a functioning efflux complex with a narrower drug specificity. mdtC corresponds to 3 loci in Pseudomonas aeruginosa PAO1 (gene name: muxC/muxB) and 3 loci in Pseudomonas aeruginosa LESB58.	aminocoumarin
contig00012	151716	152873	mdtE	0/0	100.0	99.7	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00012	152898	156011	mdtF	0/0	100.0	98.6	U00096:3660413-3663527	MdtF is the multidrug inner membrane transporter for the MdtEF-TolC efflux complex.	fluoroquinolone, macrolide, penam
contig00003	188489	189715	mdtG	0/0	100.0	99.2	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00003	198346	199554	mdtH	0/0	100.0	98.8	U00096:1125326-1124117	Multidrug resistance protein MdtH	fluoroquinolone
contig00013	91422	92453	mdtN	0/0	100.0	98.0	AP009048.1:4307588-4306556	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	acridine_dye, nucleoside
contig00013	89371	91422	mdtO	0/0	100.0	98.8	AP009048.1:4306557-4304505	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00013	87908	89374	mdtP	0/0	100.0	98.2	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00006	142312	142788	mphB	0/0	100.0	98.3	AE005174.2:3397370-3397847	The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides.	macrolide
contig00003	51653	53401	msbA	0/0	100.0	99.0	U00096.3:966620-968369	MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability.	nitroimidazole
contig00002	76806	77774	pmrF	0/0	100.0	99.4	U00096:2367070-2368039	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide
contig00002	226094	226750	QnrS1	0/0	100.0	100.0	DQ485529.1:0-657	QnrS1 is a plasmid-mediated quinolone resistance protein found in Shigella flexneri	fluoroquinolone
contig00004	36175	37662	tolC	0/0	100.0	98.4	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan
contig00002	344414	345580	ugd	0/0	100.0	95.9	U00096:2099613-2098446	PmrE is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin	peptide
contig00002	124793	126436	yojI	0/0	100.0	98.2	U00096.3:2308615-2306971	YojI mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. YojI is capable of pumping out microcin molecules. The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI.	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00006	85287	86591	(Bla)AmpC1_Ecoli	0/0	100	98.2	FN649414:2765051-2766355	(Bla)AmpC1_Ecoli	NA
contig00023	50362	51495	(Bla)AmpC2_Ecoli	0/0	100	97.2	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00010	36338	37495	(Bla)ampH_Ecoli	0/0	100	98.7	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00002	231391	232266	(Bla)blaCTX-M-15	0/0	100	100.0	JQ686199:261-1136	(Bla)blaCTX-M-15	NA
contig00007	60788	62689	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100	98.7	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA
contig00002	226094	226750	(Flq)qnr-S1	0/0	100	100.0	AB187515:9737-10393	(Flq)qnr-S1	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00002	231391	232266	blaCTX-M-15	0/0	100	100.0	NG_048935.1	class A extended-spectrum beta-lactamase CTX-M-15	CEPHALOSPORIN
contig00023	50362	51495	blaEC-13	0/0	100	99.6	NG_049079.1	class C extended-spectrum beta-lactamase EC-13	CEPHALOSPORIN
contig00002	226094	226750	qnrS1	0/0	100	100.0	NG_050543.1	quinolone resistance pentapeptide repeat protein QnrS1	QUINOLONE

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00010	127854	129047	ACRA	0/0	100.0	99.8	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00010	124682	127831	ACRB	0/0	100.0	99.1	MEG_401	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRB	NA
contig00006	117709	120822	ACRD	0/0	100.0	98.8	MEG_407	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ACRD	NA
contig00004	270325	271482	ACRE	0/0	100.0	99.0	MEG_408	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRE	NA
contig00004	271494	274598	ACRF	0/0	100.0	99.0	MEG_409	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRF	NA
contig00004	269264	269926	ACRS	0/0	100.0	98.6	MEG_415	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS	NA
contig00010	36338	37495	AMPH	0/0	100.0	98.7	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00002	300095	301947	ASMA	0/0	100.0	98.1	MEG_1180	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:ASMA	NA
contig00004	60021	60840	BACA	0/0	99.8	98.9	MEG_1189	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00002	277506	278228	BAER	0/0	100.0	99.5	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00002	278225	279628	BAES	0/0	100.0	98.7	MEG_1193	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES	NA
contig00002	151708	152898	BCR	0/0	100.0	98.2	MEG_1210	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR	NA
contig00023	50362	51495	BLAEC	0/0	100.0	99.6	MEG_1280	Drugs:betalactams:Class_C_betalactamases:BLAEC	NA
contig00027	21874	22572	CPXAR	0/0	100.0	99.4	MEG_2118	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00027	22569	23942	CPXAR	0/0	100.0	99.1	MEG_2121	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00037	15000	15632	CRP	0/0	100.0	99.2	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00001	27204	28376	EMRA	0/0	100.0	98.2	MEG_2722	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA	NA
contig00001	28393	29931	EMRB	0/0	100.0	98.5	MEG_2725	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRB	NA
contig00015	27122	28312	EMRD	0/0	100.0	99.9	MEG_2729	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD	NA
contig00006	25955	27118	EMRK	0/0	100.0	98.8	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig00001	26547	27077	EMRR	0/0	100.0	100.0	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00006	24417	25955	EMRY	0/0	100.0	98.9	MEG_2736	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRY	NA
contig00013	115182	116825	EPTA	0/0	100.0	99.2	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig00006	28153	31746	EVGS	0/0	100.0	99.5	MEG_2870	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EVGS	NA
contig00012	156374	157102	GADW	0/0	100.0	98.6	MEG_3081	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig00012	157470	158294	GADX	0/0	100.0	97.8	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00005	158443	158856	HNS	0/0	100.0	99.3	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00007	8327	8999	KDPE	0/0	99.3	97.2	MEG_3448	Drugs:Aminoglycosides:Aminoglycoside_efflux_pumps:KDPE	NA
contig00017	29288	29677	MARA	0/0	100.0	99.5	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00017	28840	29274	MARR	0/0	100.0	97.7	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00024	26130	27362	MDFA	0/0	100.0	99.2	MEG_3737	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDFA	NA
contig00002	287241	288488	MDTA	0/0	100.0	98.2	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00002	284119	287241	MDTB	0/0	100.0	98.0	MEG_3747	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTB	NA
contig00002	281041	284118	MDTC	0/0	100.0	98.1	MEG_3749	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTC	NA
contig00012	151716	152873	MDTE	0/0	100.0	99.7	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00012	152898	156011	MDTF	0/0	100.0	98.6	MEG_3752	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTF	NA
contig00003	188489	189715	MDTG	0/0	100.0	99.3	MEG_3753	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig00003	198346	199554	MDTH	0/0	100.0	98.8	MEG_3755	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTH	NA
contig00017	68323	68652	MDTI	0/0	100.0	99.7	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00017	68639	69004	MDTJ	0/0	100.0	98.9	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00009	134591	135964	MDTK	0/0	100.0	99.0	MEG_3759	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:MDTK	NA
contig00013	91422	92453	MDTN	0/0	100.0	98.0	MEG_3763	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN	NA
contig00013	89371	91422	MDTO	0/0	100.0	98.8	MEG_3764	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTO	NA
contig00013	87908	89374	MDTP	0/0	100.0	98.2	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig00006	142312	142788	MPHB	0/0	100.0	98.3	MEG_4033	Drugs:MLS:Macrolide_phosphotransferases:MPHB	NA
contig00003	51653	53401	MSBA	0/0	100.0	99.0	MEG_4061	Drugs:Multi-drug_resistance:Multi-drug_ABC_efflux_pumps:MSBA	NA
contig00008	136225	136557	MVRC	0/0	100.0	92.2	MEG_4103	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MVRC	NA
contig00007	60788	62689	PBP2	0/0	100.0	98.7	MEG_5400	Drugs:betalactams:Penicillin_binding_protein:PBP2	NA
contig00006	85287	86591	PBP4B	0/0	100.0	98.2	MEG_5409	Drugs:betalactams:Penicillin_binding_protein:PBP4B	NA
contig00002	76806	77774	PMRF	0/0	100.0	99.4	MEG_5801	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF	NA
contig00002	226094	226750	QNRS	0/0	100.0	100.0	MEG_6020	Drugs:Fluoroquinolones:Quinolone_resistance_protein_Qnr:QNRS	NA
contig00018	11905	12774	ROBA	0/0	100.0	99.1	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00013	65969	66291	SOXS	0/0	99.7	99.7	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00002	344414	345580	UGD	0/0	100.0	95.9	MEG_7328	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:UGD	NA
contig00002	124793	126436	YOGI	0/0	100.0	98.2	MEG_7842	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:YOGI	NA

ID187

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00084	1544	2347	aph(3’’)-Ib_5	0/0	100.0	100.0	AF321551	aph(3’’)-Ib	Streptomycin
contig00084	708	1544	aph(6)-Id_1	0/0	100.0	100.0	M28829	aph(6)-Id	Streptomycin
contig00057	12797	13672	blaCTX-M-15_1	0/0	100.0	100.0	AY044436	blaCTX-M-15	Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig00091	3293	4153	blaTEM-1B_1	0/0	100.0	100.0	AY458016	blaTEM-1B	Amoxicillin, Ampicillin, Cephalothin, Piperacillin, Ticarcillin
contig00125	181	663	dfrA14_5	0/0	100.0	99.6	DQ388123	dfrA14	Trimethoprim
contig00016	13339	14571	mdf(A)_1	0/0	100.0	99.9	Y08743	mdf(A)
contig00057	7500	8156	qnrS1_1	0/0	100.0	100.0	AB187515	qnrS1	Ciprofloxacin
contig00084	2408	3223	sul2_2	0/0	100.0	100.0	AY034138	sul2	Sulfamethoxazole
contig00091	711	1957	tet(A)_6	0/0	97.8	100.0	AF534183	tet(A)	Doxycycline, Tetracycline

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00001	39727	42876	acrB	0/0	100.0	100.0	U00096.3:484403-481253	Protein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug/proton antiporter.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00008	71689	74802	acrD	0/0	100.0	99.7	AP009048.1:2586250-2589364	AcrD is an aminoglycoside efflux pump expressed in E. coli. Its expression can be induced by indole and is regulated by baeRS and cpxAR.	aminoglycoside
contig00046	8641	9795	acrE	1/3	99.7	98.7	U00096:3413863-3415021	AcrE is a membrane fusion protein similar to AcrA.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00046	5525	8629	acrF	0/0	100.0	99.2	U00096:3415032-3418137	AcrF is a inner membrane transporter similar to AcrB.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00046	10194	10856	acrS	0/0	100.0	99.2	U00096:3413465-3412802	AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.	cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00084	1544	2347	APH(3’’)-Ib	0/0	100.0	99.8	AF313472:15593-16397	APH(3’’)-Ib is an aminoglycoside phosphotransferase encoded by plasmids transposons integrative conjugative elements and chromosomes in Enterobacteriaceae and Pseudomonas spp.	aminoglycoside
contig00084	708	1544	APH(6)-Id	0/0	100.0	99.9	AF024602:3155-3992	APH(6)-Id is an aminoglycoside phosphotransferase encoded by plasmids integrative conjugative elements and chromosomal genomic islands in K. pneumoniae Salmonella spp. E. coli Shigella flexneri Providencia alcalifaciens Pseudomonas spp. V. cholerae Edwardsiella tarda Pasteurella multocida and Aeromonas bestiarum	aminoglycoside
contig00002	175276	176097	bacA	0/0	100.0	100.0	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00021	24128	24850	baeR	0/0	100.0	100.0	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00021	24847	26250	baeS	0/0	100.0	100.0	AP009048:2165012-2166416	BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.	aminocoumarin, aminoglycoside
contig00012	94010	95383	cpxA	0/0	100.0	99.0	BA000007.3:4905062-4903688	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	aminocoumarin, aminoglycoside
contig00007	15081	15713	CRP	0/0	100.0	99.2	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00057	12797	13672	CTX-M-15	0/0	100.0	100.0	AY044436:1435-2311	CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family	cephalosporin
contig00125	181	663	dfrA14	0/0	100.0	99.8	EU780012:2162-2645	dfrA14 is an integron-encoded dihydrofolate reductase found in Escherichia coli	diaminopyrimidine
contig00019	26696	27868	emrA	0/0	100.0	100.0	AP009048:2810082-2811255	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	fluoroquinolone
contig00019	27885	29423	emrB	0/0	100.0	100.0	U00096:2812615-2814154	emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin.	fluoroquinolone
contig00042	5045	6100	emrK	0/0	100.0	99.9	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00019	26039	26569	emrR	0/0	100.0	100.0	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00042	3507	5045	emrY	0/0	100.0	99.0	D78168:1591-3130	emrY is a multidrug transport that moves substrates across the inner membrane of the Gram-negative E. coli. It is a homolog of emrB.	tetracycline
contig00029	37368	39011	eptA	0/0	100.0	100.0	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00001	38511	39704	Escherichia_coli_acrA	0/0	100.0	100.0	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00010	104703	105836	Escherichia_coli_ampC	0/0	100.0	100.0	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00008	116489	117793	Escherichia_coli_ampC1_beta-lactamase	0/0	100.0	98.6	FN649414.1:2765050-2766355	An ampC-like beta-lactamase identified from Escherichia coli.	cephalosporin, penam
contig00001	135618	136775	Escherichia_coli_ampH	0/0	100.0	100.0	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig00016	13339	14571	Escherichia_coli_mdfA	0/0	100.0	98.4	JQ394987:0-1233	Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter.	benzalkonium_chloride, rhodamine, tetracycline
contig00042	6624	7238	evgA	0/0	100.0	100.0	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00042	7243	10836	evgS	0/0	100.0	100.0	U00096:2484373-2487967	EvgS is a sensor protein that phosphorylates the regulatory protein EvgA. evgS corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	fluoroquinolone, macrolide, penam, tetracycline
contig00028	21921	22649	gadW	0/0	100.0	94.7	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig00028	20729	21553	gadX	0/0	100.0	100.0	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00006	119180	119593	H-NS	0/0	100.0	99.3	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00013	8068	8745	kdpE	0/0	100.0	100.0	U00096.3:721733-721055	kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding.	aminoglycoside
contig00041	33575	33958	marA	0/0	100.0	99.5	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00021	33863	35110	mdtA	0/0	100.0	98.2	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00021	30741	33863	mdtB	0/0	100.0	97.6	U00096:2155262-2158385	MdtB is a transporter that forms a heteromultimer complex with MdtC to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex.	aminocoumarin
contig00021	27663	30740	mdtC	0/0	100.0	98.4	U00096:2158385-2161463	MdtC is a transporter that forms a heteromultimer complex with MdtB to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex. In the absence of MdtB MdtC can form a homomultimer complex that results in a functioning efflux complex with a narrower drug specificity. mdtC corresponds to 3 loci in Pseudomonas aeruginosa PAO1 (gene name: muxC/muxB) and 3 loci in Pseudomonas aeruginosa LESB58.	aminocoumarin
contig00028	26150	27307	mdtE	0/0	100.0	100.0	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00028	23012	26125	mdtF	0/0	100.0	100.0	U00096:3660413-3663527	MdtF is the multidrug inner membrane transporter for the MdtEF-TolC efflux complex.	fluoroquinolone, macrolide, penam
contig00018	10295	11521	mdtG	0/0	100.0	99.4	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00018	20150	21358	mdtH	0/0	100.0	100.0	U00096:1125326-1124117	Multidrug resistance protein MdtH	fluoroquinolone
contig00061	1118	2350	mdtM	0/0	100.0	97.3	U00096.3:4568519-4567286	Multidrug resistance protein MdtM	acridine_dye, fluoroquinolone, lincosamide, nucleoside, phenicol
contig00029	6699	7730	mdtN	0/0	100.0	100.0	AP009048.1:4307588-4306556	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	acridine_dye, nucleoside
contig00029	4648	6699	mdtO	0/0	100.0	100.0	AP009048.1:4306557-4304505	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00029	3185	4651	mdtP	0/0	100.0	100.0	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00008	50480	50956	mphB	0/0	100.0	98.1	AE005174.2:3397370-3397847	The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides.	macrolide
contig00009	21382	23130	msbA	0/0	100.0	100.0	U00096.3:966620-968369	MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability.	nitroimidazole
contig00005	62225	63193	pmrF	0/0	100.0	100.0	U00096:2367070-2368039	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide
contig00057	7500	8156	QnrS1	0/0	100.0	100.0	DQ485529.1:0-657	QnrS1 is a plasmid-mediated quinolone resistance protein found in Shigella flexneri	fluoroquinolone
contig00084	2408	3223	sul2	0/0	100.0	100.0	AY055428.1:21084-20268	Sul2 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria usually found on small plasmids.	sulfonamide
contig00091	3293	4153	TEM-1	0/0	100.0	99.9	AL513383:161910-162771	TEM-1 is a broad-spectrum beta-lactamase found in many Gram-negative bacteria. Confers resistance to penicillins and first generation cephalosphorins.	cephalosporin, monobactam, penam, penem
contig00091	711	1957	tet(A)	0/0	97.8	100.0	AF534183.1:2970-4245	TetA is a tetracycline efflux pump found in many species of Gram-negative bacteria.	tetracycline
contig00002	151411	152898	tolC	0/0	100.0	100.0	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan
contig00033	47406	48572	ugd	0/0	100.0	95.5	U00096:2099613-2098446	PmrE is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin	peptide
contig00005	2099	3742	yojI	0/0	100.0	99.9	U00096.3:2308615-2306971	YojI mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. YojI is capable of pumping out microcin molecules. The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI.	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00084	1544	2347	(AGly)strA	0/0	100	99.9	AB366441:22458-23261	(AGly)strA	NA
contig00084	708	1544	(AGly)strB	0/0	100	100.0	FJ474091:264-1100	(AGly)strB	NA
contig00008	116489	117793	(Bla)AmpC1_Ecoli	0/0	100	98.6	FN649414:2765051-2766355	(Bla)AmpC1_Ecoli	NA
contig00010	104703	105836	(Bla)AmpC2_Ecoli	0/0	100	100.0	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00001	135618	136775	(Bla)ampH_Ecoli	0/0	100	100.0	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00057	12797	13672	(Bla)blaCTX-M-15	0/0	100	100.0	JQ686199:261-1136	(Bla)blaCTX-M-15	NA
contig00091	3293	4153	(Bla)blaTEM-105	0/0	100	99.9	AF516720:215-1075	(Bla)blaTEM-105	NA
contig00013	60350	62251	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100	100.0	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA
contig00057	7500	8156	(Flq)qnr-S1	0/0	100	100.0	AB187515:9737-10393	(Flq)qnr-S1	NA
contig00084	2408	3223	(Sul)sul2	0/0	100	100.0	EU360945:1617-2432	(Sul)sul2	NA
contig00091	711	1985	(Tet)tetA	0/0	100	100.0	JX424423:94438-95712	(Tet)tetA	NA
contig00091	30	680	(Tet)tetR	0/0	100	100.0	HF545434:53576-54226	(Tet)tetR	NA
contig00125	181	654	(Tmt)dfrA14	0/0	100	100.0	GU726917:72-545	(Tmt)dfrA14	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00084	1544	2371	aph(3’’)-Ib	0/0	100	100	NG_056002.2	aminoglycoside O-phosphotransferase APH(3’’)-Ib	STREPTOMYCIN
contig00084	708	1544	aph(6)-Id	0/0	100	100	NG_047464.1	aminoglycoside O-phosphotransferase APH(6)-Id	STREPTOMYCIN
contig00057	12797	13672	blaCTX-M-15	0/0	100	100	NG_048935.1	class A extended-spectrum beta-lactamase CTX-M-15	CEPHALOSPORIN
contig00010	104703	105836	blaEC	0/0	100	100	NG_047494.1	BlaEC family class C beta-lactamase	BETA-LACTAM
contig00091	3293	4153	blaTEM-1	0/0	100	100	NG_050145.1	class A broad-spectrum beta-lactamase TEM-1	BETA-LACTAM
contig00125	181	654	dfrA14	0/0	100	100	NG_056035.1	trimethoprim-resistant dihydrofolate reductase DfrA14	TRIMETHOPRIM
contig00057	7500	8156	qnrS1	0/0	100	100	NG_050543.1	quinolone resistance pentapeptide repeat protein QnrS1	QUINOLONE
contig00084	2408	3223	sul2	0/0	100	100	NG_051852.1	sulfonamide-resistant dihydropteroate synthase Sul2	SULFONAMIDE
contig00091	786	1985	tet(A)	0/0	100	100	NG_048154.1	tetracycline efflux MFS transporter Tet(A)	TETRACYCLINE

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00001	38511	39704	ACRA	0/0	100.0	100.0	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00001	39727	42876	ACRB	0/0	100.0	100.0	MEG_401	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRB	NA
contig00008	71689	74802	ACRD	0/0	100.0	99.7	MEG_407	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ACRD	NA
contig00046	8641	9795	ACRE	1/3	99.7	98.7	MEG_408	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRE	NA
contig00046	5525	8629	ACRF	0/0	100.0	99.2	MEG_409	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRF	NA
contig00046	10194	10856	ACRS	0/0	100.0	99.2	MEG_415	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS	NA
contig00010	104703	105836	AMPC	0/0	100.0	100.0	MEG_728	Drugs:betalactams:Class_C_betalactamases:AMPC	NA
contig00001	135618	136775	AMPH	0/0	100.0	100.0	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00084	1544	2371	APH3-DPRIME	0/0	100.0	100.0	MEG_1019	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH3-DPRIME	NA
contig00084	708	1544	APH6	0/0	100.0	100.0	MEG_1086	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH6	NA
contig00021	47523	49375	ASMA	0/0	100.0	98.5	MEG_1180	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:ASMA	NA
contig00002	175276	176097	BACA	0/0	100.0	100.0	MEG_1190	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00021	24128	24850	BAER	0/0	100.0	100.0	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00021	24847	26250	BAES	0/0	100.0	100.0	MEG_1193	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES	NA
contig00015	86600	87790	BCR	0/0	100.0	99.1	MEG_1210	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR	NA
contig00012	93315	94013	CPXAR	0/0	100.0	100.0	MEG_2122	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00012	94010	95383	CPXAR	0/0	100.0	100.0	MEG_2121	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00007	15081	15713	CRP	0/0	100.0	99.2	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00125	181	654	DFRA	0/0	100.0	99.8	MEG_2517	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00019	26696	27868	EMRA	0/0	100.0	100.0	MEG_2722	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA	NA
contig00019	27885	29423	EMRB	0/0	100.0	100.0	MEG_2725	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRB	NA
contig00004	91678	92868	EMRD	0/0	100.0	100.0	MEG_2729	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD	NA
contig00042	5045	6208	EMRK	0/0	100.0	99.9	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig00019	26039	26569	EMRR	0/0	100.0	100.0	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00042	3507	5045	EMRY	0/0	100.0	99.0	MEG_2736	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRY	NA
contig00029	37368	39011	EPTA	0/0	100.0	100.0	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig00042	7243	10836	EVGS	0/0	100.0	100.0	MEG_2870	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EVGS	NA
contig00028	21921	22649	GADW	0/0	100.0	100.0	MEG_3081	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig00028	20729	21553	GADX	0/0	100.0	100.0	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00006	119180	119593	HNS	0/0	100.0	99.3	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00013	8068	8745	KDPE	0/0	100.0	100.0	MEG_3448	Drugs:Aminoglycosides:Aminoglycoside_efflux_pumps:KDPE	NA
contig00041	33569	33958	MARA	0/0	100.0	99.5	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00041	33121	33555	MARR	0/0	100.0	97.7	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00016	13339	14571	MDFA	0/0	100.0	100.0	MEG_3737	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDFA	NA
contig00021	33863	35110	MDTA	0/0	100.0	98.2	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00021	30741	33863	MDTB	0/0	100.0	97.6	MEG_3747	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTB	NA
contig00021	27663	30740	MDTC	0/0	100.0	98.4	MEG_3749	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTC	NA
contig00028	26150	27307	MDTE	0/0	100.0	100.0	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00028	23012	26125	MDTF	0/0	100.0	100.0	MEG_3752	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTF	NA
contig00018	10295	11521	MDTG	0/0	100.0	100.0	MEG_3753	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig00018	20150	21358	MDTH	0/0	100.0	100.0	MEG_3755	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTH	NA
contig00032	34222	34551	MDTI	0/0	100.0	100.0	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00032	34538	34903	MDTJ	0/0	100.0	99.5	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00031	2433	3806	MDTK	0/0	100.0	98.9	MEG_3759	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:MDTK	NA
contig00061	1118	2350	MDTM	0/0	100.0	97.3	MEG_3761	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTM	NA
contig00029	6699	7730	MDTN	0/0	100.0	100.0	MEG_3763	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN	NA
contig00029	4648	6699	MDTO	0/0	100.0	100.0	MEG_3764	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTO	NA
contig00029	3185	4651	MDTP	0/0	100.0	100.0	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig00008	50480	50956	MPHB	0/0	100.0	98.1	MEG_4033	Drugs:MLS:Macrolide_phosphotransferases:MPHB	NA
contig00009	21382	23130	MSBA	0/0	100.0	100.0	MEG_4061	Drugs:Multi-drug_resistance:Multi-drug_ABC_efflux_pumps:MSBA	NA
contig00013	60350	62251	PBP2	0/0	100.0	100.0	MEG_5400	Drugs:betalactams:Penicillin_binding_protein:PBP2	NA
contig00008	116489	117793	PBP4B	0/0	100.0	98.6	MEG_5409	Drugs:betalactams:Penicillin_binding_protein:PBP4B	NA
contig00005	62225	63193	PMRF	0/0	100.0	100.0	MEG_5801	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF	NA
contig00057	7500	8156	QNRS	0/0	100.0	100.0	MEG_6020	Drugs:Fluoroquinolones:Quinolone_resistance_protein_Qnr:QNRS	NA
contig00023	49695	50564	ROBA	0/0	100.0	100.0	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00022	18450	18773	SOXS	0/0	100.0	100.0	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00084	2408	3223	SULII	0/0	100.0	100.0	MEG_6617	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULII	NA
contig00091	3275	4520	TEM	0/0	98.3	99.4	MEG_6875	Drugs:betalactams:Class_A_betalactamases:TEM	NA
contig00091	711	1985	TETA	0/0	100.0	100.0	MEG_7024	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETA	NA
contig00033	47406	48572	UGD	0/0	100.0	95.5	MEG_7328	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:UGD	NA
contig00005	2099	3742	YOGI	0/0	100.0	99.9	MEG_7842	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:YOGI	NA

ID195

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00056	137	925	aadA5_1	0/0	100.0	100	AF137361	aadA5	Streptomycin
contig00015	65021	65896	blaCTX-M-55_1	0/0	100.0	100	DQ810789	blaCTX-M-55	Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig00056	1056	1529	dfrA17_1	0/0	100.0	100	FJ460238	dfrA17	Trimethoprim
contig00029	30168	31400	mdf(A)_1	0/0	100.0	98	Y08743	mdf(A)
contig00047	3615	4271	qnrS1_1	0/0	100.0	100	AB187515	qnrS1	Ciprofloxacin
contig00043	1442	2257	sul2_2	0/0	100.0	100	AY034138	sul2	Sulfamethoxazole
contig00046	3261	4507	tet(A)_6	0/0	97.8	100	AF534183	tet(A)	Doxycycline, Tetracycline

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00056	137	925	aadA5	0/0	100.0	100.0	AF137361:63-852	aadA5 is an aminoglycoside nucleotidyltransferase gene encoded by plasmids transposons and integrons in E. coli K. pneumoniae Kluyvera georgiana P. aeruginosa and E. cloacae	aminoglycoside
contig00026	40300	43449	acrB	0/0	100.0	99.3	U00096.3:484403-481253	Protein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug/proton antiporter.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00001	519811	522924	acrD	0/0	100.0	98.9	AP009048.1:2586250-2589364	AcrD is an aminoglycoside efflux pump expressed in E. coli. Its expression can be induced by indole and is regulated by baeRS and cpxAR.	aminoglycoside
contig00011	138859	140016	acrE	0/0	100.0	99.0	U00096:3413863-3415021	AcrE is a membrane fusion protein similar to AcrA.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00011	140028	143132	acrF	0/0	100.0	98.8	U00096:3415032-3418137	AcrF is a inner membrane transporter similar to AcrB.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00011	137798	138460	acrS	0/0	100.0	99.2	U00096:3413465-3412802	AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.	cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00013	60022	60841	bacA	0/0	99.8	98.9	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00001	129169	129891	baeR	0/0	100.0	99.3	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00001	127769	129172	baeS	0/0	100.0	99.6	AP009048:2165012-2166416	BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.	aminocoumarin, aminoglycoside
contig00024	22408	23781	cpxA	0/0	100.0	98.8	BA000007.3:4905062-4903688	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	aminocoumarin, aminoglycoside
contig00003	15000	15632	CRP	0/0	100.0	99.2	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00015	65021	65896	CTX-M-55	0/0	100.0	100.0	DQ885477:0-876	CTX-M-55 is a beta-lactamase found in the Enterobacteriaceae family	cephalosporin
contig00056	1056	1529	dfrA17	0/0	100.0	100.0	DQ838665:0-474	dfrA17 is an integron-encoded dihydrofolate reductase found in Escherichia coli	diaminopyrimidine
contig00010	51982	53154	emrA	0/0	100.0	98.4	AP009048:2810082-2811255	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	fluoroquinolone
contig00010	53171	54709	emrB	0/0	100.0	99.9	U00096:2812615-2814154	emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin.	fluoroquinolone
contig00001	428091	429146	emrK	0/0	100.0	99.8	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00010	51325	51855	emrR	0/0	100.0	99.6	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00001	426553	428091	emrY	0/0	100.0	99.0	D78168:1591-3130	emrY is a multidrug transport that moves substrates across the inner membrane of the Gram-negative E. coli. It is a homolog of emrB.	tetracycline
contig00028	18477	20120	eptA	0/0	100.0	99.4	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00026	43472	44665	Escherichia_coli_acrA	0/0	100.0	99.8	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00018	98249	99382	Escherichia_coli_ampC	0/0	100.0	97.7	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00001	487410	488714	Escherichia_coli_ampC1_beta-lactamase	0/0	100.0	98.2	FN649414.1:2765050-2766355	An ampC-like beta-lactamase identified from Escherichia coli.	cephalosporin, penam
contig00009	46202	47359	Escherichia_coli_ampH	0/0	100.0	98.8	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig00029	30168	31400	Escherichia_coli_mdfA	0/0	100.0	96.5	JQ394987:0-1233	Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter.	benzalkonium_chloride, rhodamine, tetracycline
contig00001	429670	430284	evgA	0/0	100.0	99.0	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00001	430289	433882	evgS	0/0	100.0	99.4	U00096:2484373-2487967	EvgS is a sensor protein that phosphorylates the regulatory protein EvgA. evgS corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	fluoroquinolone, macrolide, penam, tetracycline
contig00003	184889	185617	gadW	0/0	100.0	94.4	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig00003	185985	186809	gadX	0/0	100.0	97.9	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00007	5176	5589	H-NS	0/0	100.0	99.0	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00012	8052	8724	kdpE	0/0	99.3	97.2	U00096.3:721733-721055	kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding.	aminoglycoside
contig00017	87066	87449	marA	0/0	100.0	99.5	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00001	118909	120156	mdtA	0/0	100.0	98.2	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00001	120156	123278	mdtB	0/0	100.0	98.0	U00096:2155262-2158385	MdtB is a transporter that forms a heteromultimer complex with MdtC to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex.	aminocoumarin
contig00001	123279	126356	mdtC	0/0	100.0	98.1	U00096:2158385-2161463	MdtC is a transporter that forms a heteromultimer complex with MdtB to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex. In the absence of MdtB MdtC can form a homomultimer complex that results in a functioning efflux complex with a narrower drug specificity. mdtC corresponds to 3 loci in Pseudomonas aeruginosa PAO1 (gene name: muxC/muxB) and 3 loci in Pseudomonas aeruginosa LESB58.	aminocoumarin
contig00003	180231	181388	mdtE	0/0	100.0	99.7	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00003	181413	184526	mdtF	0/0	100.0	98.5	U00096:3660413-3663527	MdtF is the multidrug inner membrane transporter for the MdtEF-TolC efflux complex.	fluoroquinolone, macrolide, penam
contig00006	156278	157504	mdtG	0/0	100.0	100.0	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00006	146439	147647	mdtH	0/0	100.0	98.5	U00096:1125326-1124117	Multidrug resistance protein MdtH	fluoroquinolone
contig00019	75674	76906	mdtM	0/0	100.0	96.2	U00096.3:4568519-4567286	Multidrug resistance protein MdtM	acridine_dye, fluoroquinolone, lincosamide, nucleoside, phenicol
contig00020	4215	5246	mdtN	0/0	100.0	97.9	AP009048.1:4307588-4306556	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	acridine_dye, nucleoside
contig00020	5246	7297	mdtO	0/0	100.0	98.4	AP009048.1:4306557-4304505	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00020	7294	8760	mdtP	0/0	100.0	98.2	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00001	544210	544686	mphB	0/0	100.0	98.1	AE005174.2:3397370-3397847	The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides.	macrolide
contig00005	51497	53245	msbA	0/0	100.0	99.0	U00096.3:966620-968369	MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability.	nitroimidazole
contig00001	324356	325324	pmrF	0/0	100.0	99.5	U00096:2367070-2368039	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide
contig00047	3615	4271	QnrS1	0/0	100.0	100.0	DQ485529.1:0-657	QnrS1 is a plasmid-mediated quinolone resistance protein found in Shigella flexneri	fluoroquinolone
contig00043	1442	2257	sul2	0/0	100.0	100.0	AY055428.1:21084-20268	Sul2 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria usually found on small plasmids.	sulfonamide
contig00046	3261	4507	tet(A)	0/0	97.8	100.0	AF534183.1:2970-4245	TetA is a tetracycline efflux pump found in many species of Gram-negative bacteria.	tetracycline
contig00013	36176	37663	tolC	0/0	100.0	98.5	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan
contig00001	275638	277281	yojI	0/0	100.0	98.0	U00096.3:2308615-2306971	YojI mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. YojI is capable of pumping out microcin molecules. The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI.	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00056	137	925	(AGly)aadA5	0/0	100	100.0	AF137361:64-852	(AGly)aadA5	NA
contig00001	487410	488714	(Bla)AmpC1_Ecoli	0/0	100	98.2	FN649414:2765051-2766355	(Bla)AmpC1_Ecoli	NA
contig00018	98249	99382	(Bla)AmpC2_Ecoli	0/0	100	97.7	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00009	46202	47359	(Bla)ampH_Ecoli	0/0	100	98.8	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00015	65021	65896	(Bla)blaCTX-M-55	0/0	100	100.0	HM748991:321-1196	(Bla)blaCTX-M-55	NA
contig00012	60514	62415	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100	98.7	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA
contig00047	3615	4271	(Flq)qnr-S1	0/0	100	100.0	AB187515:9737-10393	(Flq)qnr-S1	NA
contig00043	1442	2257	(Sul)sul2	0/0	100	100.0	EU360945:1617-2432	(Sul)sul2	NA
contig00046	3233	4507	(Tet)tetA	0/0	100	100.0	JX424423:94438-95712	(Tet)tetA	NA
contig00046	4538	5188	(Tet)tetR	0/0	100	99.8	HF545434:53576-54226	(Tet)tetR	NA
contig00056	1056	1529	(Tmt)dfrA17	0/0	100	100.0	AB126604:98-571	(Tmt)dfrA17	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00056	137	925	aadA5	0/0	100	100.0	NG_047357.1	ANT(3’’)-Ia family aminoglycoside nucleotidyltransferase AadA5	STREPTOMYCIN
contig00015	65021	65896	blaCTX-M-55	0/0	100	100.0	NG_049006.1	class A extended-spectrum beta-lactamase CTX-M-55	CEPHALOSPORIN
contig00018	98249	99382	blaEC-18	0/0	100	99.7	NG_049083.1	class C extended-spectrum beta-lactamase EC-18	CEPHALOSPORIN
contig00056	1056	1529	dfrA17	0/0	100	99.8	NG_047710.1	trimethoprim-resistant dihydrofolate reductase DfrA17	TRIMETHOPRIM
contig00047	3615	4271	qnrS1	0/0	100	100.0	NG_050543.1	quinolone resistance pentapeptide repeat protein QnrS1	QUINOLONE
contig00043	1442	2257	sul2	0/0	100	100.0	NG_051852.1	sulfonamide-resistant dihydropteroate synthase Sul2	SULFONAMIDE
contig00046	3233	4432	tet(A)	0/0	100	100.0	NG_048154.1	tetracycline efflux MFS transporter Tet(A)	TETRACYCLINE

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00026	43472	44665	ACRA	0/0	100.0	99.8	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00026	40300	43449	ACRB	0/0	100.0	99.3	MEG_401	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRB	NA
contig00001	519811	522924	ACRD	0/0	100.0	98.9	MEG_407	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ACRD	NA
contig00011	138859	140016	ACRE	0/0	100.0	99.0	MEG_408	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRE	NA
contig00011	140028	143132	ACRF	0/0	100.0	98.8	MEG_409	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRF	NA
contig00011	137798	138460	ACRS	0/0	100.0	99.2	MEG_415	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS	NA
contig00009	46202	47359	AMPH	0/0	100.0	98.8	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00056	137	925	ANT3-DPRIME	0/0	100.0	100.0	MEG_928	Drugs:Aminoglycosides:Aminoglycoside_O-nucleotidyltransferases:ANT3-DPRIME	NA
contig00001	105450	107302	ASMA	0/0	100.0	98.4	MEG_1180	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:ASMA	NA
contig00013	60022	60841	BACA	0/0	99.8	98.9	MEG_1189	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00001	129169	129891	BAER	0/0	100.0	99.3	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00001	127769	129172	BAES	0/0	100.0	99.6	MEG_1193	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES	NA
contig00001	249176	250366	BCR	0/0	100.0	97.5	MEG_1210	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR	NA
contig00018	98249	99382	BLAEC	0/0	100.0	99.7	MEG_1279	Drugs:betalactams:Class_C_betalactamases:BLAEC	NA
contig00024	21713	22411	CPXAR	0/0	100.0	100.0	MEG_2122	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00024	22408	23781	CPXAR	0/0	100.0	99.6	MEG_2121	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00003	15000	15632	CRP	0/0	100.0	99.2	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00056	1056	1529	DFRA	0/0	100.0	100.0	MEG_2547	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00010	51982	53154	EMRA	0/0	100.0	98.4	MEG_2722	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA	NA
contig00010	53171	54709	EMRB	0/0	100.0	99.9	MEG_2725	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRB	NA
contig00004	103365	104555	EMRD	0/0	100.0	99.9	MEG_2729	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD	NA
contig00001	428091	429254	EMRK	0/0	100.0	99.8	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig00010	51325	51855	EMRR	0/0	100.0	99.6	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00001	426553	428091	EMRY	0/0	100.0	99.0	MEG_2736	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRY	NA
contig00028	18477	20120	EPTA	0/0	100.0	99.4	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig00001	430289	433882	EVGS	0/0	100.0	99.4	MEG_2870	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EVGS	NA
contig00003	184889	185617	GADW	0/0	100.0	98.6	MEG_3081	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig00003	185985	186809	GADX	0/0	100.0	97.9	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00007	5176	5589	HNS	0/0	100.0	99.0	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00012	8052	8724	KDPE	0/0	99.3	97.2	MEG_3448	Drugs:Aminoglycosides:Aminoglycoside_efflux_pumps:KDPE	NA
contig00017	87060	87449	MARA	0/0	100.0	99.5	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00017	86612	87046	MARR	0/0	100.0	97.5	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00029	30168	31400	MDFA	0/0	100.0	98.1	MEG_3737	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDFA	NA
contig00001	118909	120156	MDTA	0/0	100.0	98.2	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00001	120156	123278	MDTB	0/0	100.0	98.0	MEG_3747	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTB	NA
contig00001	123279	126356	MDTC	0/0	100.0	98.1	MEG_3749	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTC	NA
contig00003	180231	181388	MDTE	0/0	100.0	99.7	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00003	181413	184526	MDTF	0/0	100.0	98.5	MEG_3752	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTF	NA
contig00006	156278	157504	MDTG	0/0	100.0	100.0	MEG_3754	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig00006	146439	147647	MDTH	0/0	100.0	98.5	MEG_3755	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTH	NA
contig00002	377209	377538	MDTI	0/0	100.0	99.4	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00002	376857	377222	MDTJ	0/0	100.0	99.7	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00002	305718	307091	MDTK	0/0	100.0	99.0	MEG_3759	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:MDTK	NA
contig00019	75674	76906	MDTM	0/0	100.0	96.2	MEG_3761	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTM	NA
contig00020	4215	5246	MDTN	0/0	100.0	97.9	MEG_3763	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN	NA
contig00020	5246	7297	MDTO	0/0	100.0	98.4	MEG_3764	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTO	NA
contig00020	7294	8760	MDTP	0/0	100.0	98.2	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig00001	544210	544686	MPHB	0/0	100.0	98.1	MEG_4033	Drugs:MLS:Macrolide_phosphotransferases:MPHB	NA
contig00005	51497	53245	MSBA	0/0	100.0	99.0	MEG_4061	Drugs:Multi-drug_resistance:Multi-drug_ABC_efflux_pumps:MSBA	NA
contig00012	60514	62415	PBP2	0/0	100.0	98.7	MEG_5400	Drugs:betalactams:Penicillin_binding_protein:PBP2	NA
contig00001	487410	488714	PBP4B	0/0	100.0	98.2	MEG_5409	Drugs:betalactams:Penicillin_binding_protein:PBP4B	NA
contig00001	324356	325324	PMRF	0/0	100.0	99.5	MEG_5801	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF	NA
contig00047	3615	4271	QNRS	0/0	100.0	100.0	MEG_6020	Drugs:Fluoroquinolones:Quinolone_resistance_protein_Qnr:QNRS	NA
contig00019	11911	12780	ROBA	0/0	100.0	99.1	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00020	30375	30698	SOXS	0/0	100.0	99.7	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00043	1442	2257	SULII	0/0	100.0	100.0	MEG_6617	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULII	NA
contig00046	3233	4507	TETA	0/0	100.0	100.0	MEG_7024	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETA	NA
contig00001	275638	277281	YOGI	0/0	100.0	98.0	MEG_7842	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:YOGI	NA

ID197

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00081	1694	2554	aac(3)-IIa_1	0/0	100	99.8	X51534	aac(3)-IIa	Gentamicin, Tobramycin
contig00078	1539	2138	aac(6’)-Ib-cr_1	0/0	100	100.0	DQ303918	aac(6’)-Ib-cr	Ciprofloxacin
contig00070	1702	2490	aadA5_1	0/0	100	99.9	AF137361	aadA5	Streptomycin
contig00069	1222	2097	blaCTX-M-15_1	0/0	100	100.0	AY044436	blaCTX-M-15	Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig00078	578	1408	blaOXA-1_1	0/0	100	100.0	HQ170510	blaOXA-1	Amoxicillin, Amoxicillin+Clavulanic_acid, Ampicillin, Ampicillin+Clavulanic_acid, Cefepime, Piperacillin, Piperacillin+Tazobactam
contig00070	2621	3094	dfrA17_1	0/0	100	100.0	FJ460238	dfrA17	Trimethoprim
contig00001	147439	148671	mdf(A)_1	0/0	100	99.9	Y08743	mdf(A)
contig00099	69	990	mph(A)_2	1/1	100	99.7	U36578	mph(A)	Erythromycin, Azithromycin, Spiramycin, Telithromycin
contig00070	316	1182	sul1_5	0/0	100	99.9	EU780013	sul1	Sulfamethoxazole
contig00066	1998	3203	tet(B)_2	0/0	100	100.0	AF326777	tet(B)	Doxycycline, Tetracycline, Minocycline

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00081	1694	2554	AAC(3)-IIe	0/0	100.0	99.5	EU022315.1:0-861	AAC(3)-IIe is a plasmid-encoded aminoglycoside acetyltransferase in E. coli	aminoglycoside
contig00078	1539	2138	AAC(6’)-Ib-cr	0/0	100.0	100.0	DQ303918:0-600	AAC(6’)-Ib-cr is an aminoglycoside acetyltransferase encoded by plasmids transposons integrons in Enterobacteriaceae. The aac(6’)-Ib-cr variant gene can induce resistance against aminoglycoside and fluoroquinolone simultaneously	aminoglycoside, fluoroquinolone
contig00070	1702	2490	aadA5	0/0	100.0	99.9	AF137361:63-852	aadA5 is an aminoglycoside nucleotidyltransferase gene encoded by plasmids transposons and integrons in E. coli K. pneumoniae Kluyvera georgiana P. aeruginosa and E. cloacae	aminoglycoside
contig00005	41368	44517	acrB	0/0	100.0	100.0	U00096.3:484403-481253	Protein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug/proton antiporter.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00004	148083	151196	acrD	0/0	100.0	98.8	AP009048.1:2586250-2589364	AcrD is an aminoglycoside efflux pump expressed in E. coli. Its expression can be induced by indole and is regulated by baeRS and cpxAR.	aminoglycoside
contig00063	5844	8948	acrF	0/0	100.0	100.0	U00096:3415032-3418137	AcrF is a inner membrane transporter similar to AcrB.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00036	602	1264	acrS	0/0	100.0	100.0	U00096:3413465-3412802	AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.	cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00011	70353	71172	bacA	0/0	99.8	98.5	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00019	58159	58881	baeR	0/0	100.0	100.0	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00019	58878	60281	baeS	0/0	100.0	99.9	AP009048:2165012-2166416	BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.	aminocoumarin, aminoglycoside
contig00013	61576	62949	cpxA	0/0	100.0	99.0	BA000007.3:4905062-4903688	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	aminocoumarin, aminoglycoside
contig00008	46847	47479	CRP	0/0	100.0	99.7	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00069	1222	2097	CTX-M-15	0/0	100.0	100.0	AY044436:1435-2311	CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family	cephalosporin
contig00070	2621	3094	dfrA17	0/0	100.0	100.0	DQ838665:0-474	dfrA17 is an integron-encoded dihydrofolate reductase found in Escherichia coli	diaminopyrimidine
contig00009	58703	59875	emrA	0/0	100.0	97.9	AP009048:2810082-2811255	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	fluoroquinolone
contig00009	59892	61430	emrB	0/0	100.0	98.6	U00096:2812615-2814154	emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin.	fluoroquinolone
contig00002	178458	179513	emrK	0/0	100.0	98.0	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00009	58046	58576	emrR	0/0	100.0	99.4	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00002	176920	178458	emrY	0/0	100.0	97.7	D78168:1591-3130	emrY is a multidrug transport that moves substrates across the inner membrane of the Gram-negative E. coli. It is a homolog of emrB.	tetracycline
contig00006	81600	83243	eptA	0/0	100.0	99.9	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00005	40152	41345	Escherichia_coli_acrA	0/0	100.0	100.0	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00006	38239	39372	Escherichia_coli_ampC	0/0	100.0	97.3	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00051	25613	26911	Escherichia_coli_ampC1_beta-lactamase	0/0	99.5	96.1	FN649414.1:2765050-2766355	An ampC-like beta-lactamase identified from Escherichia coli.	cephalosporin, penam
contig00005	129484	130641	Escherichia_coli_ampH	0/0	100.0	100.0	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig00001	147439	148671	Escherichia_coli_mdfA	0/0	100.0	98.4	JQ394987:0-1233	Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter.	benzalkonium_chloride, rhodamine, tetracycline
contig00002	180037	180651	evgA	0/0	100.0	99.2	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00002	180656	184249	evgS	0/0	100.0	96.8	U00096:2484373-2487967	EvgS is a sensor protein that phosphorylates the regulatory protein EvgA. evgS corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	fluoroquinolone, macrolide, penam, tetracycline
contig00040	1784	2512	gadW	0/0	100.0	94.7	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig00040	592	1416	gadX	0/0	100.0	100.0	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00010	40941	41354	H-NS	0/0	100.0	99.3	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00015	8068	8745	kdpE	0/0	100.0	100.0	U00096.3:721733-721055	kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding.	aminoglycoside
contig00003	150943	151326	marA	0/0	100.0	100.0	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00019	67894	69141	mdtA	0/0	100.0	100.0	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00019	64772	67894	mdtB	0/0	100.0	99.8	U00096:2155262-2158385	MdtB is a transporter that forms a heteromultimer complex with MdtC to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex.	aminocoumarin
contig00019	61694	64771	mdtC	0/0	100.0	99.9	U00096:2158385-2161463	MdtC is a transporter that forms a heteromultimer complex with MdtB to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex. In the absence of MdtB MdtC can form a homomultimer complex that results in a functioning efflux complex with a narrower drug specificity. mdtC corresponds to 3 loci in Pseudomonas aeruginosa PAO1 (gene name: muxC/muxB) and 3 loci in Pseudomonas aeruginosa LESB58.	aminocoumarin
contig00040	6013	7170	mdtE	0/0	100.0	100.0	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00040	2875	5988	mdtF	0/0	100.0	100.0	U00096:3660413-3663527	MdtF is the multidrug inner membrane transporter for the MdtEF-TolC efflux complex.	fluoroquinolone, macrolide, penam
contig00035	16609	17835	mdtG	0/0	100.0	99.4	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00035	26464	27672	mdtH	0/0	100.0	99.9	U00096:1125326-1124117	Multidrug resistance protein MdtH	fluoroquinolone
contig00023	70066	71298	mdtM	0/0	100.0	96.3	U00096.3:4568519-4567286	Multidrug resistance protein MdtM	acridine_dye, fluoroquinolone, lincosamide, nucleoside, phenicol
contig00006	112981	114012	mdtN	0/0	100.0	100.0	AP009048.1:4307588-4306556	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	acridine_dye, nucleoside
contig00006	114012	116063	mdtO	0/0	100.0	100.0	AP009048.1:4306557-4304505	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00006	116060	117526	mdtP	0/0	100.0	100.0	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00099	69	974	mphA	0/0	100.0	100.0	D16251.1:2531-1625	The mphA gene encodes for resistance enzyme MPH(2’)-I which preferentially inactivate 14-membered macrolides (e.g.erythromycin telithromycin roxithromycin) over 16-membered macrolides (e.g.tylosin spiramycin). It phosphorylates macrolides at 2’-OH hydroxyl of desosamine sugar of macrolides in a GTP-dependent manner.	macrolide
contig00004	126902	127376	mphB	0/0	99.6	96.2	AE005174.2:3397370-3397847	The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides.	macrolide
contig00001	230387	232135	msbA	0/0	100.0	100.0	U00096.3:966620-968369	MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability.	nitroimidazole
contig00078	578	1408	OXA-1	0/0	100.0	100.0	JN420336.1:2230-1399	OXA-1 is a beta-lactamase found in E. coli	cephalosporin, penam
contig00002	63945	64913	pmrF	0/0	100.0	98.0	U00096:2367070-2368039	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide
contig00070	316	1155	sul1	0/0	100.0	100.0	JF969163:1053-1893	Sul1 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria. It is linked to other resistance genes of class 1 integrons.	sulfonamide
contig00066	1998	3203	tet(B)	0/0	100.0	99.8	AB089595:0-1206	Tet(B) is a tetracycline efflux protein expressed in many Gram-negative bacteria. It confers resistance to tetracycline doxycycline and minocycline but not tigecycline.	tetracycline
contig00011	46586	48073	tolC	0/0	100.0	99.9	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan
contig00002	2069	3712	yojI	0/0	100.0	100.0	U00096.3:2308615-2306971	YojI mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. YojI is capable of pumping out microcin molecules. The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI.	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00081	1694	2554	(AGly)aac3-IIa	0/0	100.0	99.8	X51534:91-951	(AGly)aac3-IIa	NA
contig00070	1702	2490	(AGly)aadA5	0/0	100.0	99.9	AF137361:64-852	(AGly)aadA5	NA
contig00051	25613	26911	(Bla)AmpC1_Ecoli	0/0	99.5	96.1	FN649414:2765051-2766355	(Bla)AmpC1_Ecoli	NA
contig00006	38239	39372	(Bla)AmpC2_Ecoli	0/0	100.0	97.3	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00005	129484	130641	(Bla)ampH_Ecoli	0/0	100.0	100.0	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00069	1222	2097	(Bla)blaCTX-M-15	0/0	100.0	100.0	JQ686199:261-1136	(Bla)blaCTX-M-15	NA
contig00078	578	1408	(Bla)blaOXA-1	0/0	100.0	100.0	JQ682867:1-831	(Bla)blaOXA-1	NA
contig00015	60155	62056	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100.0	100.0	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA
contig00099	69	974	(MLS)mph(A)	0/0	100.0	100.0	DQ445270:1626-2531	(MLS)mph(A)	NA
contig00070	316	1155	(Sul)sul1	0/0	100.0	100.0	AF071413:6700-7539	(Sul)sul1	NA
contig00066	1998	3203	(Tet)tetB	0/0	100.0	99.7	AB089594:1-1206	(Tet)tetB	NA
contig00070	2621	3094	(Tmt)dfrA17	0/0	100.0	100.0	AB126604:98-571	(Tmt)dfrA17	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00081	1694	2554	aac(3)-IIe	0/0	100	99.8	NG_047244.1	aminoglycoside N-acetyltransferase AAC(3)-IIe	GENTAMICIN
contig00078	1539	2093	aac(6’)-Ib-D181Y	0/0	100	99.8	NG_067946.1	AAC(6’)-Ib family aminoglycoside 6’-N-acetyltransferase	AMIKACIN, KANAMYCIN, TOBRAMYCIN
contig00070	1702	2490	aadA5	0/0	100	99.9	NG_047357.1	ANT(3’’)-Ia family aminoglycoside nucleotidyltransferase AadA5	STREPTOMYCIN
contig00069	1222	2097	blaCTX-M-15	0/0	100	100.0	NG_048935.1	class A extended-spectrum beta-lactamase CTX-M-15	CEPHALOSPORIN
contig00006	38239	39372	blaEC-15	0/0	100	98.5	NG_049081.1	class C extended-spectrum beta-lactamase EC-15	CEPHALOSPORIN
contig00078	578	1408	blaOXA-1	0/0	100	100.0	NG_049392.1	oxacillin-hydrolyzing class D beta-lactamase OXA-1	CEPHALOSPORIN
contig00070	2621	3094	dfrA17	0/0	100	99.8	NG_047710.1	trimethoprim-resistant dihydrofolate reductase DfrA17	TRIMETHOPRIM
contig00099	69	990	mph(A)	1/1	100	99.7	NG_047986.1	Mph(A) family macrolide 2’-phosphotransferase	MACROLIDE
contig00070	316	1155	sul1	0/0	100	100.0	NG_048082.1	sulfonamide-resistant dihydropteroate synthase Sul1	SULFONAMIDE
contig00066	1998	3203	tet(B)	0/0	100	100.0	NG_048163.1	tetracycline efflux MFS transporter Tet(B)	TETRACYCLINE

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00081	1694	2554	AAC3	0/0	100.0	99.8	MEG_44	Drugs:Aminoglycosides:Aminoglycoside_N-acetyltransferases:AAC3	NA
contig00005	40152	41345	ACRA	0/0	100.0	100.0	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00005	41368	44517	ACRB	0/0	100.0	100.0	MEG_401	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRB	NA
contig00004	148083	151196	ACRD	0/0	100.0	98.8	MEG_407	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ACRD	NA
contig00063	5844	8948	ACRF	0/0	100.0	100.0	MEG_409	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRF	NA
contig00036	602	1264	ACRS	0/0	100.0	100.0	MEG_415	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS	NA
contig00005	129484	130641	AMPH	0/0	100.0	100.0	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00070	1702	2490	ANT3-DPRIME	0/0	100.0	99.9	MEG_928	Drugs:Aminoglycosides:Aminoglycoside_O-nucleotidyltransferases:ANT3-DPRIME	NA
contig00019	81481	83334	ASMA	0/0	100.0	96.9	MEG_1180	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:ASMA	NA
contig00011	70353	71172	BACA	0/0	99.8	98.8	MEG_1189	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00019	58159	58881	BAER	0/0	100.0	100.0	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00019	58878	60281	BAES	0/0	100.0	99.9	MEG_1193	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES	NA
contig00017	85725	86915	BCR	0/0	100.0	100.0	MEG_1210	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR	NA
contig00006	38239	39372	BLAEC	0/0	100.0	98.5	MEG_1282	Drugs:betalactams:Class_C_betalactamases:BLAEC	NA
contig00013	60881	61579	CPXAR	0/0	100.0	100.0	MEG_2122	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00013	61576	62949	CPXAR	0/0	100.0	100.0	MEG_2121	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00008	46847	47479	CRP	0/0	100.0	99.7	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00101	62	1004	CTX	0/0	100.0	98.2	MEG_2435	Drugs:betalactams:Class_A_betalactamases:CTX	NA
contig00070	2621	3094	DFRA	0/0	100.0	100.0	MEG_2547	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00009	58703	59875	EMRA	0/0	100.0	97.9	MEG_2722	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA	NA
contig00009	59892	61430	EMRB	0/0	100.0	98.6	MEG_2725	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRB	NA
contig00038	43241	44431	EMRD	0/0	100.0	100.0	MEG_2729	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD	NA
contig00002	178458	179621	EMRK	0/0	100.0	98.2	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig00009	58046	58576	EMRR	0/0	100.0	99.4	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00002	176920	178458	EMRY	0/0	100.0	97.7	MEG_2736	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRY	NA
contig00006	81600	83243	EPTA	0/0	100.0	99.9	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig00002	180656	184249	EVGS	0/0	100.0	97.2	MEG_2869	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EVGS	NA
contig00040	1784	2512	GADW	0/0	100.0	100.0	MEG_3081	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig00040	592	1416	GADX	0/0	100.0	100.0	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00010	40941	41354	HNS	0/0	100.0	99.3	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00015	8068	8745	KDPE	0/0	100.0	100.0	MEG_3448	Drugs:Aminoglycosides:Aminoglycoside_efflux_pumps:KDPE	NA
contig00003	150943	151332	MARA	0/0	100.0	100.0	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00003	151346	151780	MARR	0/0	100.0	100.0	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00001	147439	148671	MDFA	0/0	100.0	100.0	MEG_3737	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDFA	NA
contig00019	67894	69141	MDTA	0/0	100.0	100.0	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00019	64772	67894	MDTB	0/0	100.0	99.8	MEG_3747	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTB	NA
contig00019	61694	64771	MDTC	0/0	100.0	99.9	MEG_3749	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTC	NA
contig00040	6013	7170	MDTE	0/0	100.0	100.0	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00040	2875	5988	MDTF	0/0	100.0	100.0	MEG_3752	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTF	NA
contig00035	16609	17835	MDTG	0/0	100.0	100.0	MEG_3753	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig00035	26464	27672	MDTH	0/0	100.0	99.9	MEG_3755	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTH	NA
contig00003	118221	118550	MDTI	0/0	100.0	100.0	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00003	117869	118234	MDTJ	0/0	100.0	99.5	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00003	46467	47840	MDTK	0/0	100.0	100.0	MEG_3759	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:MDTK	NA
contig00023	70066	71298	MDTM	0/0	100.0	96.3	MEG_3761	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTM	NA
contig00006	112981	114012	MDTN	0/0	100.0	100.0	MEG_3763	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN	NA
contig00006	114012	116063	MDTO	0/0	100.0	100.0	MEG_3764	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTO	NA
contig00006	116060	117526	MDTP	0/0	100.0	100.0	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig00099	69	990	MPHA	1/1	100.0	99.7	MEG_4030	Drugs:MLS:Macrolide_phosphotransferases:MPHA	NA
contig00004	126902	127376	MPHB	0/0	99.6	96.2	MEG_4033	Drugs:MLS:Macrolide_phosphotransferases:MPHB	NA
contig00001	230387	232135	MSBA	0/0	100.0	100.0	MEG_4061	Drugs:Multi-drug_resistance:Multi-drug_ABC_efflux_pumps:MSBA	NA
contig00078	578	1408	OXA	0/0	100.0	100.0	MEG_4980	Drugs:betalactams:Class_D_betalactamases:OXA	NA
contig00015	60155	62056	PBP2	0/0	100.0	100.0	MEG_5400	Drugs:betalactams:Penicillin_binding_protein:PBP2	NA
contig00051	25613	26911	PBP4B	0/0	99.5	96.1	MEG_5409	Drugs:betalactams:Penicillin_binding_protein:PBP4B	NA
contig00002	63945	64913	PMRF	0/0	100.0	98.0	MEG_5801	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF	NA
contig00023	21724	22593	ROBA	0/0	100.0	99.0	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00006	139143	139466	SOXS	0/0	100.0	100.0	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00070	189	1156	SULI	0/0	100.0	100.0	MEG_6615	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULI	NA
contig00066	1998	3203	TETB	0/0	100.0	100.0	MEG_7052	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETB	NA
contig00066	3997	4413	TETD	0/0	100.0	100.0	MEG_7070	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETD	NA
contig00002	2069	3712	YOGI	0/0	100.0	100.0	MEG_7842	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:YOGI	NA

ID199

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00034	7566	8367	aadA2_1	0/0	97.9	99.9	NC_010870	aadA2	Streptomycin
contig00006	121783	122658	blaCTX-M-15_1	0/0	100.0	100.0	AY044436	blaCTX-M-15	Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig00034	1	660	catA1_1	0/0	100.0	99.8	V00622	catA1	Chloramphenicol
contig00034	6671	7168	dfrA12_8	0/0	100.0	100.0	AM040708	dfrA12	Trimethoprim
contig00051	266	1029	erm(B)_18	2/2	100.0	99.0	X66468	erm(B)	Erythromycin, Lincomycin, Clindamycin, Quinupristin, Pristinamycin_IA, Virginiamycin_S
contig00007	90087	91319	mdf(A)_1	0/0	100.0	98.5	Y08743	mdf(A)
contig00058	69	999	mph(A)_2	2/10	100.0	98.7	U36578	mph(A)	Erythromycin, Azithromycin, Spiramycin, Telithromycin
contig00034	8845	9711	sul1_5	0/0	100.0	99.9	EU780013	sul1	Sulfamethoxazole
contig00050	802	2007	tet(B)_2	0/0	100.0	100.0	AF326777	tet(B)	Doxycycline, Tetracycline, Minocycline

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00034	7588	8367	aadA2	0/0	100.0	99.9	AF156486:5012-5792	aadA2 is an aminoglycoside nucleotidyltransferase gene encoded by plasmids and integrons in K. pneumoniae Salmonella spp. Corynebacterium glutamicum C. freundii and Aeromonas spp.	aminoglycoside
contig00004	215392	218541	acrB	0/0	100.0	99.1	U00096.3:484403-481253	Protein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug/proton antiporter.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00011	135682	138795	acrD	0/0	100.0	99.0	AP009048.1:2586250-2589364	AcrD is an aminoglycoside efflux pump expressed in E. coli. Its expression can be induced by indole and is regulated by baeRS and cpxAR.	aminoglycoside
contig00001	8755	9912	acrE	0/0	100.0	98.8	U00096:3413863-3415021	AcrE is a membrane fusion protein similar to AcrA.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00001	5639	8743	acrF	0/0	100.0	98.9	U00096:3415032-3418137	AcrF is a inner membrane transporter similar to AcrB.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00001	10311	10973	acrS	0/0	100.0	98.9	U00096:3413465-3412802	AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.	cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00001	219264	220083	bacA	0/0	99.8	98.9	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00015	48811	49533	baeR	0/0	100.0	99.5	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00015	47411	48814	baeS	0/0	100.0	98.7	AP009048:2165012-2166416	BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.	aminocoumarin, aminoglycoside
contig00034	1	660	catI	0/0	100.0	99.8	V00622:243-903	catI is a chromosome and transposon-encoded variant of the cat gene found in Escherichia coli and Acinetobacter baumannii	phenicol
contig00013	67580	68953	cpxA	0/0	100.0	98.8	BA000007.3:4905062-4903688	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	aminocoumarin, aminoglycoside
contig00012	15257	15889	CRP	0/0	100.0	99.2	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00006	121783	122658	CTX-M-15	0/0	100.0	100.0	AY044436:1435-2311	CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family	cephalosporin
contig00034	6671	7168	dfrA12	0/0	100.0	100.0	GU585907.1:22103-21605	dfrA12 is an integron-encoded dihydrofolate reductase found in Vibrio cholerae	diaminopyrimidine
contig00008	58784	59956	emrA	0/0	100.0	98.2	AP009048:2810082-2811255	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	fluoroquinolone
contig00008	59973	61511	emrB	0/0	100.0	99.2	U00096:2812615-2814154	emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin.	fluoroquinolone
contig00010	168957	170012	emrK	0/0	100.0	99.7	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00008	58127	58657	emrR	0/0	100.0	100.0	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00010	167419	168957	emrY	0/0	100.0	98.7	D78168:1591-3130	emrY is a multidrug transport that moves substrates across the inner membrane of the Gram-negative E. coli. It is a homolog of emrB.	tetracycline
contig00016	93098	94741	eptA	0/0	100.0	99.4	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00051	292	1037	ErmB	1/1	99.9	99.2	AF242872.1:2131-2878	ErmB confers the MLSb phenotype. Similar to ErmC expression of ErmB is inducible by erythromycin. The leader peptide causes attenuation of the mRNA and stabilizes the structure preventing further translation. When erythromycin is present it binds the leader peptide causing a change in conformation allowing for the expression of ErmB.	lincosamide, macrolide, streptogramin
contig00004	214176	215369	Escherichia_coli_acrA	0/0	100.0	99.8	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00016	49758	50891	Escherichia_coli_ampC	0/0	100.0	97.5	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00011	169913	171217	Escherichia_coli_ampC1_beta-lactamase	0/0	100.0	98.2	FN649414.1:2765050-2766355	An ampC-like beta-lactamase identified from Escherichia coli.	cephalosporin, penam
contig00004	303413	304570	Escherichia_coli_ampH	0/0	100.0	98.7	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig00007	90087	91319	Escherichia_coli_mdfA	0/0	100.0	96.9	JQ394987:0-1233	Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter.	benzalkonium_chloride, rhodamine, tetracycline
contig00010	170536	171150	evgA	0/0	100.0	99.0	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00010	171155	174748	evgS	0/0	100.0	99.4	U00096:2484373-2487967	EvgS is a sensor protein that phosphorylates the regulatory protein EvgA. evgS corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	fluoroquinolone, macrolide, penam, tetracycline
contig00012	182191	182919	gadW	0/0	100.0	94.8	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig00012	183287	184111	gadX	0/0	100.0	97.9	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00002	177105	177518	H-NS	0/0	100.0	99.3	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00004	8162	8834	kdpE	0/0	99.3	97.3	U00096.3:721733-721055	kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding.	aminoglycoside
contig00005	238627	239010	marA	0/0	100.0	99.2	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00015	38551	39798	mdtA	0/0	100.0	98.0	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00015	39798	42920	mdtB	0/0	100.0	98.7	U00096:2155262-2158385	MdtB is a transporter that forms a heteromultimer complex with MdtC to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex.	aminocoumarin
contig00015	42921	45998	mdtC	0/0	100.0	98.2	U00096:2158385-2161463	MdtC is a transporter that forms a heteromultimer complex with MdtB to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex. In the absence of MdtB MdtC can form a homomultimer complex that results in a functioning efflux complex with a narrower drug specificity. mdtC corresponds to 3 loci in Pseudomonas aeruginosa PAO1 (gene name: muxC/muxB) and 3 loci in Pseudomonas aeruginosa LESB58.	aminocoumarin
contig00012	177533	178690	mdtE	0/0	100.0	99.7	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00012	178715	181828	mdtF	0/0	100.0	98.6	U00096:3660413-3663527	MdtF is the multidrug inner membrane transporter for the MdtEF-TolC efflux complex.	fluoroquinolone, macrolide, penam
contig00002	379153	380379	mdtG	0/0	100.0	99.2	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00002	369314	370522	mdtH	0/0	100.0	98.9	U00096:1125326-1124117	Multidrug resistance protein MdtH	fluoroquinolone
contig00003	298836	300068	mdtM	0/0	100.0	95.5	U00096.3:4568519-4567286	Multidrug resistance protein MdtM	acridine_dye, fluoroquinolone, lincosamide, nucleoside, phenicol
contig00014	4267	5298	mdtN	0/0	100.0	98.0	AP009048.1:4307588-4306556	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	acridine_dye, nucleoside
contig00014	5298	7349	mdtO	0/0	100.0	98.7	AP009048.1:4306557-4304505	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00014	7346	8812	mdtP	0/0	100.0	98.2	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00058	69	971	mphA	0/0	99.7	100.0	D16251.1:2531-1625	The mphA gene encodes for resistance enzyme MPH(2’)-I which preferentially inactivate 14-membered macrolides (e.g.erythromycin telithromycin roxithromycin) over 16-membered macrolides (e.g.tylosin spiramycin). It phosphorylates macrolides at 2’-OH hydroxyl of desosamine sugar of macrolides in a GTP-dependent manner.	macrolide
contig00011	113929	114403	mphB	0/0	99.6	97.5	AE005174.2:3397370-3397847	The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides.	macrolide
contig00017	24523	26271	msbA	0/0	100.0	99.0	U00096.3:966620-968369	MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability.	nitroimidazole
contig00010	57891	58859	pmrF	0/0	100.0	99.7	U00096:2367070-2368039	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide
contig00034	8872	9711	sul1	0/0	100.0	100.0	JF969163:1053-1893	Sul1 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria. It is linked to other resistance genes of class 1 integrons.	sulfonamide
contig00050	802	2007	tet(B)	0/0	100.0	99.8	AB089595:0-1206	Tet(B) is a tetracycline efflux protein expressed in many Gram-negative bacteria. It confers resistance to tetracycline doxycycline and minocycline but not tigecycline.	tetracycline
contig00001	242442	243929	tolC	0/0	100.0	98.5	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan
contig00010	2013	3656	yojI	0/0	100.0	98.2	U00096.3:2308615-2306971	YojI mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. YojI is capable of pumping out microcin molecules. The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI.	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00034	7588	8367	(AGly)aadA2	0/0	100.0	99.9	X68227:66-945	(AGly)aadA2	NA
contig00011	169913	171217	(Bla)AmpC1_Ecoli	0/0	100.0	98.2	FN649414:2765051-2766355	(Bla)AmpC1_Ecoli	NA
contig00016	49758	50891	(Bla)AmpC2_Ecoli	0/0	100.0	97.5	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00004	303413	304570	(Bla)ampH_Ecoli	0/0	100.0	98.7	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00006	121783	122658	(Bla)blaCTX-M-15	0/0	100.0	100.0	JQ686199:261-1136	(Bla)blaCTX-M-15	NA
contig00004	60623	62524	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100.0	99.4	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA
contig00051	292	1029	(MLS)erm(B)	0/0	100.0	99.6	M11180:714-1451	(MLS)erm(B)	NA
contig00058	69	971	(MLS)mph(A)	0/0	99.7	100.0	DQ445270:1626-2531	(MLS)mph(A)	NA
contig00034	1	660	(Phe)catA1	0/0	100.0	99.8	V00622:244-903	(Phe)catA1	NA
contig00034	8872	9711	(Sul)sul1	0/0	100.0	100.0	AF071413:6700-7539	(Sul)sul1	NA
contig00050	802	2007	(Tet)tetB	0/0	100.0	99.7	AB089594:1-1206	(Tet)tetB	NA
contig00034	6671	7168	(Tmt)dfrA12	0/0	100.0	100.0	Z21672:310-807	(Tmt)dfrA12	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00034	7576	8367	aadA2	0/0	100	100.0	NG_047343.1	ANT(3’’)-Ia family aminoglycoside nucleotidyltransferase AadA2	STREPTOMYCIN
contig00006	121783	122658	blaCTX-M-15	0/0	100	100.0	NG_048935.1	class A extended-spectrum beta-lactamase CTX-M-15	CEPHALOSPORIN
contig00016	49758	50891	blaEC-18	0/0	100	99.2	NG_049083.1	class C extended-spectrum beta-lactamase EC-18	CEPHALOSPORIN
contig00034	1	660	catA1	0/0	100	99.8	NG_047582.1	type A-1 chloramphenicol O-acetyltransferase	CHLORAMPHENICOL
contig00034	6671	7168	dfrA12	0/0	100	100.0	NG_047689.1	trimethoprim-resistant dihydrofolate reductase DfrA12	TRIMETHOPRIM
contig00051	292	1029	erm(B)	0/0	100	99.9	NG_047804.1	23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(B)	MACROLIDE
contig00058	69	999	mph(A)	2/10	100	98.7	NG_047986.1	Mph(A) family macrolide 2’-phosphotransferase	MACROLIDE
contig00034	8872	9711	sul1	0/0	100	100.0	NG_048082.1	sulfonamide-resistant dihydropteroate synthase Sul1	SULFONAMIDE
contig00050	802	2007	tet(B)	0/0	100	100.0	NG_048163.1	tetracycline efflux MFS transporter Tet(B)	TETRACYCLINE

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00004	214176	215369	ACRA	0/0	100.0	99.8	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00004	215392	218541	ACRB	0/0	100.0	99.1	MEG_401	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRB	NA
contig00011	135682	138795	ACRD	0/0	100.0	99.0	MEG_407	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ACRD	NA
contig00001	8755	9912	ACRE	0/0	100.0	98.8	MEG_408	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRE	NA
contig00001	5639	8743	ACRF	0/0	100.0	98.9	MEG_409	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRF	NA
contig00001	10311	10973	ACRS	0/0	100.0	98.9	MEG_415	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS	NA
contig00004	303413	304570	AMPH	0/0	100.0	98.7	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00034	7566	8367	ANT3-DPRIME	0/0	97.9	99.9	MEG_975	Drugs:Aminoglycosides:Aminoglycoside_O-nucleotidyltransferases:ANT3-DPRIME	NA
contig00015	24763	26616	ASMA	0/0	100.0	96.1	MEG_1180	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:ASMA	NA
contig00001	219264	220083	BACA	0/0	99.8	98.9	MEG_1189	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00015	48811	49533	BAER	0/0	100.0	99.5	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00015	47411	48814	BAES	0/0	100.0	98.7	MEG_1193	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES	NA
contig00020	23471	24661	BCR	0/0	100.0	98.2	MEG_1210	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR	NA
contig00016	49758	50891	BLAEC	0/0	100.0	99.2	MEG_1279	Drugs:betalactams:Class_C_betalactamases:BLAEC	NA
contig00034	1	660	CATA	0/0	100.0	100.0	MEG_1584	Drugs:Phenicol:Chloramphenicol_acetyltransferases:CATA	NA
contig00013	66885	67583	CPXAR	0/0	100.0	99.7	MEG_2118	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00013	67580	68953	CPXAR	0/0	100.0	99.4	MEG_2121	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00012	15257	15889	CRP	0/0	100.0	99.2	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00034	6671	7168	DFRA	0/0	100.0	100.0	MEG_2551	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00008	58784	59956	EMRA	0/0	100.0	98.2	MEG_2722	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA	NA
contig00008	59973	61511	EMRB	0/0	100.0	99.2	MEG_2725	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRB	NA
contig00006	174944	176134	EMRD	0/0	100.0	99.9	MEG_2729	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD	NA
contig00010	168957	170120	EMRK	0/0	100.0	99.7	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig00008	58127	58657	EMRR	0/0	100.0	100.0	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00010	167419	168957	EMRY	0/0	100.0	98.8	MEG_2736	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRY	NA
contig00016	93098	94741	EPTA	0/0	100.0	99.4	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig00051	266	1029	ERMB	2/2	100.0	99.0	MEG_2801	Drugs:MLS:23S_rRNA_methyltransferases:ERMB	NA
contig00010	171155	174748	EVGS	0/0	100.0	99.4	MEG_2870	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EVGS	NA
contig00012	182191	182919	GADW	0/0	100.0	99.0	MEG_3081	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig00012	183287	184111	GADX	0/0	100.0	97.9	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00002	177105	177518	HNS	0/0	100.0	99.3	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00004	8162	8834	KDPE	0/0	99.3	97.3	MEG_3448	Drugs:Aminoglycosides:Aminoglycoside_efflux_pumps:KDPE	NA
contig00005	238627	239016	MARA	0/0	100.0	99.2	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00005	239030	239464	MARR	0/0	100.0	97.9	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00007	90087	91319	MDFA	0/0	100.0	98.5	MEG_3737	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDFA	NA
contig00015	38551	39798	MDTA	0/0	100.0	98.0	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00015	39798	42920	MDTB	0/0	100.0	98.7	MEG_3747	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTB	NA
contig00015	42921	45998	MDTC	0/0	100.0	98.2	MEG_3749	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTC	NA
contig00012	177533	178690	MDTE	0/0	100.0	99.7	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00012	178715	181828	MDTF	0/0	100.0	98.6	MEG_3752	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTF	NA
contig00002	379153	380379	MDTG	0/0	100.0	99.3	MEG_3753	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig00002	369314	370522	MDTH	0/0	100.0	98.9	MEG_3755	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTH	NA
contig00005	199652	199981	MDTI	0/0	100.0	99.7	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00005	199300	199665	MDTJ	0/0	100.0	98.1	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00005	127979	129352	MDTK	0/0	100.0	99.1	MEG_3759	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:MDTK	NA
contig00003	298836	300068	MDTM	0/0	100.0	95.5	MEG_3761	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTM	NA
contig00014	4267	5298	MDTN	0/0	100.0	98.0	MEG_3763	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN	NA
contig00014	5298	7349	MDTO	0/0	100.0	98.7	MEG_3764	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTO	NA
contig00014	7346	8812	MDTP	0/0	100.0	98.2	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig00058	69	999	MPHA	2/10	100.0	98.7	MEG_4030	Drugs:MLS:Macrolide_phosphotransferases:MPHA	NA
contig00011	113929	114403	MPHB	0/0	99.6	97.5	MEG_4033	Drugs:MLS:Macrolide_phosphotransferases:MPHB	NA
contig00017	24523	26271	MSBA	0/0	100.0	99.0	MEG_4061	Drugs:Multi-drug_resistance:Multi-drug_ABC_efflux_pumps:MSBA	NA
contig00004	60623	62524	PBP2	0/0	100.0	99.4	MEG_5400	Drugs:betalactams:Penicillin_binding_protein:PBP2	NA
contig00011	169913	171217	PBP4B	0/0	100.0	98.2	MEG_5409	Drugs:betalactams:Penicillin_binding_protein:PBP4B	NA
contig00010	57891	58859	PMRF	0/0	100.0	99.7	MEG_5801	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF	NA
contig00003	229077	229946	ROBA	0/0	100.0	99.4	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00014	30428	30750	SOXS	0/0	99.7	99.7	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00034	8871	9838	SULI	0/0	100.0	100.0	MEG_6615	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULI	NA
contig00050	802	2007	TETB	0/0	100.0	100.0	MEG_7052	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETB	NA
contig00010	2013	3656	YOGI	0/0	100.0	98.2	MEG_7842	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:YOGI	NA

ID208

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00581	1694	2554	aac(3)-IIa_1	0/0	100	99.8	X51534	aac(3)-IIa	Gentamicin, Tobramycin
contig00620	1539	2138	aac(6’)-Ib-cr_1	0/0	100	100.0	DQ303918	aac(6’)-Ib-cr	Ciprofloxacin
contig00612	94	882	aadA5_1	0/0	100	100.0	AF137361	aadA5	Streptomycin
contig00014	106338	107213	blaCTX-M-15_1	0/0	100	100.0	AY044436	blaCTX-M-15	Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig00297	5698	6843	blaMIR-6_1	0/0	100	99.7	JQ664733	blaMIR-6
contig00620	578	1408	blaOXA-1_1	0/0	100	100.0	HQ170510	blaOXA-1	Amoxicillin, Amoxicillin+Clavulanic_acid, Ampicillin, Ampicillin+Clavulanic_acid, Cefepime, Piperacillin, Piperacillin+Tazobactam
contig00003	49	909	blaTEM-1B_1	0/0	100	100.0	AY458016	blaTEM-1B	Amoxicillin, Ampicillin, Cephalothin, Piperacillin, Ticarcillin
contig00705	945	1418	dfrA15_2	0/0	100	100.0	AF221900	dfrA15	Trimethoprim
contig00612	1013	1486	dfrA17_1	0/0	100	100.0	FJ460238	dfrA17	Trimethoprim
contig00644	266	1029	erm(B)_18	2/2	100	99.0	X66468	erm(B)	Erythromycin, Lincomycin, Clindamycin, Quinupristin, Pristinamycin_IA, Virginiamycin_S
contig00597	1819	2244	fosA_7	0/0	100	95.8	AEXB01000013	fosA	Fosfomycin
contig00004	66771	68003	mdf(A)_1	0/0	100	98.3	Y08743	mdf(A)
contig00753	67	997	mph(A)_2	2/10	100	98.7	U36578	mph(A)	Erythromycin, Azithromycin, Spiramycin, Telithromycin
contig00525	385	1251	sul1_5	0/0	100	99.9	EU780013	sul1	Sulfamethoxazole

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00581	1694	2554	AAC(3)-IIe	0/0	100.0	99.5	EU022315.1:0-861	AAC(3)-IIe is a plasmid-encoded aminoglycoside acetyltransferase in E. coli	aminoglycoside
contig00620	1539	2138	AAC(6’)-Ib-cr	0/0	100.0	100.0	DQ303918:0-600	AAC(6’)-Ib-cr is an aminoglycoside acetyltransferase encoded by plasmids transposons integrons in Enterobacteriaceae. The aac(6’)-Ib-cr variant gene can induce resistance against aminoglycoside and fluoroquinolone simultaneously	aminoglycoside, fluoroquinolone
contig00612	94	882	aadA5	0/0	100.0	100.0	AF137361:63-852	aadA5 is an aminoglycoside nucleotidyltransferase gene encoded by plasmids transposons and integrons in E. coli K. pneumoniae Kluyvera georgiana P. aeruginosa and E. cloacae	aminoglycoside
contig00002	118149	121298	acrB	0/0	100.0	99.0	U00096.3:484403-481253	Protein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug/proton antiporter.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00010	63159	66272	acrD	0/0	100.0	98.7	AP009048.1:2586250-2589364	AcrD is an aminoglycoside efflux pump expressed in E. coli. Its expression can be induced by indole and is regulated by baeRS and cpxAR.	aminoglycoside
contig00008	8762	9919	acrE	0/0	100.0	98.2	U00096:3413863-3415021	AcrE is a membrane fusion protein similar to AcrA.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00008	5646	8750	acrF	0/0	100.0	97.5	U00096:3415032-3418137	AcrF is a inner membrane transporter similar to AcrB.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00008	10318	10980	acrS	0/0	100.0	97.6	U00096:3413465-3412802	AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.	cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00017	26444	27263	bacA	0/0	99.8	97.0	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00063	10730	11451	baeR	0/0	99.9	98.1	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00063	9330	10733	baeS	0/0	100.0	96.4	AP009048:2165012-2166416	BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.	aminocoumarin, aminoglycoside
contig00019	22628	24001	cpxA	0/0	100.0	98.8	BA000007.3:4905062-4903688	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	aminocoumarin, aminoglycoside
contig00014	15001	15633	CRP	0/0	100.0	99.2	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00014	106338	107213	CTX-M-15	0/0	100.0	100.0	AY044436:1435-2311	CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family	cephalosporin
contig00705	945	1418	dfrA15	0/0	100.0	100.0	KF534911:39-513	dfrA15 is an integron-encoded dihydrofolate reductase found in Vibrio cholerae	diaminopyrimidine
contig00612	1013	1486	dfrA17	0/0	100.0	100.0	DQ838665:0-474	dfrA17 is an integron-encoded dihydrofolate reductase found in Escherichia coli	diaminopyrimidine
contig00023	54374	55546	emrA	0/0	100.0	98.1	AP009048:2810082-2811255	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	fluoroquinolone
contig00023	55563	57101	emrB	0/0	100.0	98.5	U00096:2812615-2814154	emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin.	fluoroquinolone
contig00001	166248	167303	emrK	0/0	100.0	96.9	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00023	53717	54247	emrR	0/0	100.0	99.4	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00001	164710	166248	emrY	0/0	100.0	98.0	D78168:1591-3130	emrY is a multidrug transport that moves substrates across the inner membrane of the Gram-negative E. coli. It is a homolog of emrB.	tetracycline
contig00047	12043	13686	eptA	0/0	100.0	98.2	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00644	292	1037	ErmB	1/1	99.9	99.2	AF242872.1:2131-2878	ErmB confers the MLSb phenotype. Similar to ErmC expression of ErmB is inducible by erythromycin. The leader peptide causes attenuation of the mRNA and stabilizes the structure preventing further translation. When erythromycin is present it binds the leader peptide causing a change in conformation allowing for the expression of ErmB.	lincosamide, macrolide, streptogramin
contig00002	121321	122514	Escherichia_coli_acrA	0/0	100.0	99.0	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00005	129751	130884	Escherichia_coli_ampC	0/0	100.0	98.1	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00010	28626	29930	Escherichia_coli_ampC1_beta-lactamase	0/0	100.0	95.2	FN649414.1:2765050-2766355	An ampC-like beta-lactamase identified from Escherichia coli.	cephalosporin, penam
contig00002	30743	31900	Escherichia_coli_ampH	0/0	100.0	97.3	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig00004	66771	68003	Escherichia_coli_mdfA	0/0	100.0	96.8	JQ394987:0-1233	Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter.	benzalkonium_chloride, rhodamine, tetracycline
contig00001	167826	168440	evgA	0/0	100.0	99.3	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00001	168445	172038	evgS	0/0	100.0	96.6	U00096:2484373-2487967	EvgS is a sensor protein that phosphorylates the regulatory protein EvgA. evgS corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	fluoroquinolone, macrolide, penam, tetracycline
contig00597	1819	2244	FosA2	0/0	100.0	91.8	EU487198:216-642	An enzyme that confers resistance to fosfomycin in Enterobacter cloacae by breaking the epoxide ring of the molecule. It depends on the cofactors Manganese (II) and Potassium and uses Glutathione (GSH) as the nucleophilic molecule.	fosfomycin
contig00003	90677	91405	gadW	0/0	100.0	95.9	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig00003	91774	92598	gadX	0/0	100.0	93.9	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00087	1492	1905	H-NS	0/0	100.0	99.5	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00013	69445	70122	kdpE	0/0	100.0	95.6	U00096.3:721733-721055	kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding.	aminoglycoside
contig00041	27850	28233	marA	0/0	100.0	100.0	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00063	470	1717	mdtA	0/0	100.0	97.4	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00063	1717	4839	mdtB	0/0	100.0	96.7	U00096:2155262-2158385	MdtB is a transporter that forms a heteromultimer complex with MdtC to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex.	aminocoumarin
contig00063	4840	7917	mdtC	0/0	100.0	97.1	U00096:2158385-2161463	MdtC is a transporter that forms a heteromultimer complex with MdtB to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex. In the absence of MdtB MdtC can form a homomultimer complex that results in a functioning efflux complex with a narrower drug specificity. mdtC corresponds to 3 loci in Pseudomonas aeruginosa PAO1 (gene name: muxC/muxB) and 3 loci in Pseudomonas aeruginosa LESB58.	aminocoumarin
contig00003	86019	87176	mdtE	0/0	100.0	99.0	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00003	87201	90314	mdtF	0/0	100.0	98.4	U00096:3660413-3663527	MdtF is the multidrug inner membrane transporter for the MdtEF-TolC efflux complex.	fluoroquinolone, macrolide, penam
contig00022	73604	74830	mdtG	0/0	100.0	98.3	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00022	63765	64973	mdtH	0/0	100.0	98.0	U00096:1125326-1124117	Multidrug resistance protein MdtH	fluoroquinolone
contig00025	37676	38908	mdtM	0/0	100.0	95.0	U00096.3:4568519-4567286	Multidrug resistance protein MdtM	acridine_dye, fluoroquinolone, lincosamide, nucleoside, phenicol
contig00027	17076	18107	mdtN	0/0	100.0	97.7	AP009048.1:4307588-4306556	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	acridine_dye, nucleoside
contig00027	18107	20158	mdtO	0/0	100.0	96.6	AP009048.1:4306557-4304505	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00027	20155	21621	mdtP	0/0	100.0	96.5	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00297	5698	6843	MIR-6	0/0	100.0	99.7	JQ664733:0-1146	MIR-6 is a beta-lactamase. From the Lahey list of MIR beta-lactamases.	cephalosporin, monobactam
contig00753	67	969	mphA	0/0	99.7	100.0	D16251.1:2531-1625	The mphA gene encodes for resistance enzyme MPH(2’)-I which preferentially inactivate 14-membered macrolides (e.g.erythromycin telithromycin roxithromycin) over 16-membered macrolides (e.g.tylosin spiramycin). It phosphorylates macrolides at 2’-OH hydroxyl of desosamine sugar of macrolides in a GTP-dependent manner.	macrolide
contig00010	86979	87453	mphB	0/0	99.6	96.2	AE005174.2:3397370-3397847	The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides.	macrolide
contig00009	51469	53217	msbA	0/0	100.0	98.9	U00096.3:966620-968369	MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability.	nitroimidazole
contig00620	578	1408	OXA-1	0/0	100.0	100.0	JN420336.1:2230-1399	OXA-1 is a beta-lactamase found in E. coli	cephalosporin, penam
contig00001	61868	62836	pmrF	0/0	100.0	97.9	U00096:2367070-2368039	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide
contig00307	4154	4505	ramA	0/0	93.9	93.2	JQ727668:0-375	RamA (resistance antibiotic multiple) is a positive regulator of AcrAB-TolC and leads to high level multidrug resistance in Klebsiella pneumoniae Salmonella enterica and Enterobacter aerugenes increasing the expression of both the mar operon as well as AcrAB. RamA also decreases OmpF expression.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00525	412	1251	sul1	0/0	100.0	100.0	JF969163:1053-1893	Sul1 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria. It is linked to other resistance genes of class 1 integrons.	sulfonamide
contig00003	49	909	TEM-1	0/0	100.0	99.9	AL513383:161910-162771	TEM-1 is a broad-spectrum beta-lactamase found in many Gram-negative bacteria. Confers resistance to penicillins and first generation cephalosphorins.	cephalosporin, monobactam, penam, penem
contig00017	4629	6116	tolC	0/0	100.0	97.9	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan
contig00160	11221	12387	ugd	0/0	100.0	96.4	U00096:2099613-2098446	PmrE is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin	peptide
contig00001	47	1690	yojI	0/0	100.0	97.8	U00096.3:2308615-2306971	YojI mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. YojI is capable of pumping out microcin molecules. The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI.	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00581	1694	2554	(AGly)aac3-IIa	0/0	100.0	99.8	X51534:91-951	(AGly)aac3-IIa	NA
contig00705	52	853	(AGly)aadA1-pm	0/0	96.5	99.9	JQ690540:7968-8798	(AGly)aadA1-pm	NA
contig00612	94	882	(AGly)aadA5	0/0	100.0	100.0	AF137361:64-852	(AGly)aadA5	NA
contig00010	28626	29930	(Bla)AmpC1_Ecoli	0/0	100.0	95.2	FN649414:2765051-2766355	(Bla)AmpC1_Ecoli	NA
contig00005	129751	130884	(Bla)AmpC2_Ecoli	0/0	100.0	98.1	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00002	30743	31900	(Bla)ampH_Ecoli	0/0	100.0	97.3	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00014	106338	107213	(Bla)blaCTX-M-15	0/0	100.0	100.0	JQ686199:261-1136	(Bla)blaCTX-M-15	NA
contig00297	5698	6843	(Bla)blaMIR-6	0/0	100.0	99.7	JQ664733:1-1146	(Bla)blaMIR-6	NA
contig00620	578	1408	(Bla)blaOXA-1	0/0	100.0	100.0	JQ682867:1-831	(Bla)blaOXA-1	NA
contig00003	49	909	(Bla)blaTEM-105	0/0	100.0	99.9	AF516720:215-1075	(Bla)blaTEM-105	NA
contig00088	11297	13198	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100.0	98.4	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA
contig00597	1819	2244	(Fcyn)FosA2	0/0	100.0	91.8	EU487198:217-642	(Fcyn)FosA2	NA
contig00644	292	1029	(MLS)erm(B)	0/0	100.0	99.6	M11180:714-1451	(MLS)erm(B)	NA
contig00753	67	969	(MLS)mph(A)	0/0	99.7	100.0	DQ445270:1626-2531	(MLS)mph(A)	NA
contig00525	412	1251	(Sul)sul1	0/0	100.0	100.0	AF071413:6700-7539	(Sul)sul1	NA
contig00705	945	1418	(Tmt)dfrA15b	0/0	100.0	99.2	AJ867237:177-650	(Tmt)dfrA15b	NA
contig00612	1013	1486	(Tmt)dfrA17	0/0	100.0	100.0	AB126604:98-571	(Tmt)dfrA17	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00581	1694	2554	aac(3)-IIe	0/0	100	99.8	NG_047244.1	aminoglycoside N-acetyltransferase AAC(3)-IIe	GENTAMICIN
contig00620	1539	2093	aac(6’)-Ib-D181Y	0/0	100	99.8	NG_067946.1	AAC(6’)-Ib family aminoglycoside 6’-N-acetyltransferase	AMIKACIN, KANAMYCIN, TOBRAMYCIN
contig00705	52	843	aadA1	0/0	100	99.9	NG_052266.1	ANT(3’’)-Ia family aminoglycoside nucleotidyltransferase AadA1	STREPTOMYCIN
contig00612	94	882	aadA5	0/0	100	100.0	NG_047357.1	ANT(3’’)-Ia family aminoglycoside nucleotidyltransferase AadA5	STREPTOMYCIN
contig00014	106338	107213	blaCTX-M-15	0/0	100	100.0	NG_048935.1	class A extended-spectrum beta-lactamase CTX-M-15	CEPHALOSPORIN
contig00005	129751	130884	blaEC-19	0/0	100	99.9	NG_049084.1	class C extended-spectrum beta-lactamase EC-19	CEPHALOSPORIN
contig00297	5698	6843	blaMIR-20	0/0	100	100.0	NG_050722.1	cephalosporin-hydrolyzing class C beta-lactamase MIR-20	CEPHALOSPORIN
contig00620	578	1408	blaOXA-1	0/0	100	100.0	NG_049392.1	oxacillin-hydrolyzing class D beta-lactamase OXA-1	CEPHALOSPORIN
contig00003	49	909	blaTEM-1	0/0	100	100.0	NG_050145.1	class A broad-spectrum beta-lactamase TEM-1	BETA-LACTAM
contig00705	945	1418	dfrA15	0/0	100	100.0	NG_047702.1	trimethoprim-resistant dihydrofolate reductase DfrA15	TRIMETHOPRIM
contig00612	1013	1486	dfrA17	0/0	100	99.8	NG_047710.1	trimethoprim-resistant dihydrofolate reductase DfrA17	TRIMETHOPRIM
contig00644	292	1029	erm(B)	0/0	100	99.9	NG_047804.1	23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(B)	MACROLIDE
contig00597	1819	2244	fosA	0/0	100	95.5	NG_050405.1	fosfomycin resistance glutathione transferase FosA	FOSFOMYCIN
contig00753	67	997	mph(A)	2/10	100	98.7	NG_047986.1	Mph(A) family macrolide 2’-phosphotransferase	MACROLIDE
contig00163	5314	8433	oqxB9	0/0	99	90.1	NG_050458.1	multidrug efflux RND transporter permease subunit OqxB9	PHENICOL, QUINOLONE
contig00525	412	1251	sul1	0/0	100	100.0	NG_048082.1	sulfonamide-resistant dihydropteroate synthase Sul1	SULFONAMIDE

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00581	1694	2554	AAC3	0/0	100.0	99.8	MEG_44	Drugs:Aminoglycosides:Aminoglycoside_N-acetyltransferases:AAC3	NA
contig00002	121321	122514	ACRA	0/0	100.0	99.0	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00002	118149	121298	ACRB	0/0	100.0	99.0	MEG_401	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRB	NA
contig00010	63159	66272	ACRD	0/0	100.0	98.7	MEG_407	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ACRD	NA
contig00008	8762	9919	ACRE	0/0	100.0	98.2	MEG_408	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRE	NA
contig00008	5646	8750	ACRF	0/0	100.0	97.5	MEG_409	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRF	NA
contig00008	10318	10980	ACRS	0/0	100.0	97.6	MEG_415	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS	NA
contig00002	30743	31900	AMPH	0/0	100.0	97.3	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00612	94	882	ANT3-DPRIME	0/0	100.0	100.0	MEG_928	Drugs:Aminoglycosides:Aminoglycoside_O-nucleotidyltransferases:ANT3-DPRIME	NA
contig00705	52	853	ANT3-DPRIME	0/0	96.5	99.9	MEG_915	Drugs:Aminoglycosides:Aminoglycoside_O-nucleotidyltransferases:ANT3-DPRIME	NA
contig00035	11329	13181	ASMA	0/0	100.0	98.3	MEG_1180	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:ASMA	NA
contig00017	26444	27263	BACA	0/0	99.8	97.2	MEG_1189	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00063	10730	11451	BAER	0/0	99.9	98.1	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00063	9330	10733	BAES	0/0	100.0	96.4	MEG_1193	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES	NA
contig00024	49010	50200	BCR	0/0	100.0	96.6	MEG_1210	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR	NA
contig00005	129751	130884	BLAEC	0/0	100.0	99.9	MEG_1277	Drugs:betalactams:Class_C_betalactamases:BLAEC	NA
contig00019	21933	22631	CPXAR	0/0	100.0	99.4	MEG_2118	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00019	22628	24001	CPXAR	0/0	100.0	99.0	MEG_2121	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00014	15001	15633	CRP	0/0	100.0	99.2	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00612	1013	1486	DFRA	0/0	100.0	100.0	MEG_2547	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00705	945	1418	DFRA	0/0	100.0	99.4	MEG_2492	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00023	54374	55546	EMRA	0/0	100.0	98.1	MEG_2722	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA	NA
contig00023	55563	57101	EMRB	0/0	100.0	98.5	MEG_2725	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRB	NA
contig00018	89485	90675	EMRD	0/0	100.0	97.8	MEG_2729	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD	NA
contig00001	166248	167411	EMRK	0/0	100.0	96.7	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig00023	53717	54247	EMRR	0/0	100.0	99.4	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00001	164710	166248	EMRY	0/0	100.0	98.0	MEG_2736	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRY	NA
contig00047	12043	13686	EPTA	0/0	100.0	98.2	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig00644	266	1029	ERMB	2/2	100.0	99.0	MEG_2801	Drugs:MLS:23S_rRNA_methyltransferases:ERMB	NA
contig00001	168445	172038	EVGS	0/0	100.0	97.1	MEG_2869	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EVGS	NA
contig00597	1665	2244	FOSA	0/0	99.7	92.6	MEG_2990	Drugs:Fosfomycin:Fosfomycin_thiol_transferases:FOSA	NA
contig00003	90677	91405	GADW	0/0	100.0	97.0	MEG_3081	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig00003	91774	92598	GADX	0/0	100.0	93.9	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00087	1492	1905	HNS	0/0	100.0	99.5	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00013	69445	70122	KDPE	0/0	100.0	95.6	MEG_3448	Drugs:Aminoglycosides:Aminoglycoside_efflux_pumps:KDPE	NA
contig00041	27844	28233	MARA	0/0	100.0	100.0	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00041	27395	27829	MARR	0/0	100.0	98.6	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00004	66771	68003	MDFA	0/0	100.0	98.4	MEG_3737	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDFA	NA
contig00063	470	1717	MDTA	0/0	100.0	97.4	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00063	1717	4839	MDTB	0/0	100.0	96.7	MEG_3747	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTB	NA
contig00063	4840	7917	MDTC	0/0	100.0	97.1	MEG_3749	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTC	NA
contig00003	86019	87176	MDTE	0/0	100.0	99.0	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00003	87201	90314	MDTF	0/0	100.0	98.4	MEG_3752	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTF	NA
contig00022	73604	74830	MDTG	0/0	100.0	98.7	MEG_3753	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig00022	63765	64973	MDTH	0/0	100.0	98.0	MEG_3755	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTH	NA
contig00050	21791	22120	MDTI	0/0	100.0	99.7	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00050	22107	22472	MDTJ	0/0	100.0	98.6	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00011	86990	88362	MDTK	0/0	99.9	97.9	MEG_3759	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:MDTK	NA
contig00025	37676	38908	MDTM	0/0	100.0	95.0	MEG_3761	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTM	NA
contig00027	17076	18107	MDTN	0/0	100.0	97.7	MEG_3763	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN	NA
contig00027	18107	20158	MDTO	0/0	100.0	96.6	MEG_3764	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTO	NA
contig00027	20155	21621	MDTP	0/0	100.0	96.5	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig00297	5685	6844	MIR	0/0	100.0	99.4	MEG_3972	Drugs:betalactams:Class_C_betalactamases:MIR	NA
contig00753	67	997	MPHA	2/10	100.0	98.7	MEG_4030	Drugs:MLS:Macrolide_phosphotransferases:MPHA	NA
contig00010	86979	87453	MPHB	0/0	99.6	96.2	MEG_4033	Drugs:MLS:Macrolide_phosphotransferases:MPHB	NA
contig00009	51469	53217	MSBA	0/0	100.0	98.9	MEG_4061	Drugs:Multi-drug_resistance:Multi-drug_ABC_efflux_pumps:MSBA	NA
contig00163	5314	8433	OQXB	0/0	99.0	90.1	MEG_4359	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:OQXB	NA
contig00620	578	1408	OXA	0/0	100.0	100.0	MEG_4980	Drugs:betalactams:Class_D_betalactamases:OXA	NA
contig00088	11297	13198	PBP2	0/0	100.0	98.4	MEG_5400	Drugs:betalactams:Penicillin_binding_protein:PBP2	NA
contig00010	28626	29930	PBP4B	0/0	100.0	95.2	MEG_5409	Drugs:betalactams:Penicillin_binding_protein:PBP4B	NA
contig00001	61868	62836	PMRF	0/0	100.0	97.9	MEG_5801	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF	NA
contig00525	71	418	QACEDELTA1	0/0	100.0	100.0	MEG_5829	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:QACEDELTA1	NA
contig00307	4154	4505	RAMA	0/0	93.9	93.2	MEG_6044	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:RAMA	NA
contig00072	6646	7515	ROBA	0/0	100.0	99.0	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00027	41822	42144	SOXS	0/0	99.7	97.8	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00525	411	1378	SULI	0/0	100.0	100.0	MEG_6615	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULI	NA
contig00160	11221	12387	UGD	0/0	100.0	96.4	MEG_7328	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:UGD	NA
contig00001	47	1690	YOGI	0/0	100.0	97.8	MEG_7842	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:YOGI	NA

ID214

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00093	1406	2266	aac(3)-IId_1	0/0	100	99.9	EU022314	aac(3)-IId	Gentamicin, Tobramycin
contig00109	1538	2137	aac(6’)-Ib-cr_1	0/0	100	100.0	DQ303918	aac(6’)-Ib-cr	Ciprofloxacin
contig00085	2474	3262	aadA5_1	0/0	100	100.0	AF137361	aadA5	Streptomycin
contig00087	5399	6178	aph(3’’)-Ib_5	0/0	97	100.0	AF321551	aph(3’’)-Ib	Streptomycin
contig00087	4563	5399	aph(6)-Id_1	0/0	100	100.0	M28829	aph(6)-Id	Streptomycin
contig00090	1871	2746	blaCTX-M-15_1	0/0	100	100.0	AY044436	blaCTX-M-15	Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig00109	577	1407	blaOXA-1_1	0/0	100	100.0	HQ170510	blaOXA-1	Amoxicillin, Amoxicillin+Clavulanic_acid, Ampicillin, Ampicillin+Clavulanic_acid, Cefepime, Piperacillin, Piperacillin+Tazobactam
contig00082	1940	2800	blaTEM-1B_1	0/0	100	100.0	AY458016	blaTEM-1B	Amoxicillin, Ampicillin, Cephalothin, Piperacillin, Ticarcillin
contig00092	221	880	catA1_1	0/0	100	99.8	V00622	catA1	Chloramphenicol
contig00085	1870	2343	dfrA17_1	0/0	100	100.0	FJ460238	dfrA17	Trimethoprim
contig00006	30138	31370	mdf(A)_1	0/0	100	99.9	Y08743	mdf(A)
contig00082	6011	6932	mph(A)_2	1/1	100	99.6	U36578	mph(A)	Erythromycin, Azithromycin, Spiramycin, Telithromycin
contig00085	3782	4648	sul1_5	0/0	100	99.9	EU780013	sul1	Sulfamethoxazole
contig00087	85	900	sul2_2	0/0	100	100.0	AY034138	sul2	Sulfamethoxazole
contig00096	1065	2270	tet(B)_2	0/0	100	100.0	AF326777	tet(B)	Doxycycline, Tetracycline, Minocycline

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00093	1406	2266	AAC(3)-IId	0/0	100.0	99.9	EU022314.1:0-861	AAC(3)-IId is a plasmid-encoded aminoglycoside acetyltransferase in E. coli	aminoglycoside
contig00109	1538	2137	AAC(6’)-Ib-cr	0/0	100.0	100.0	DQ303918:0-600	AAC(6’)-Ib-cr is an aminoglycoside acetyltransferase encoded by plasmids transposons integrons in Enterobacteriaceae. The aac(6’)-Ib-cr variant gene can induce resistance against aminoglycoside and fluoroquinolone simultaneously	aminoglycoside, fluoroquinolone
contig00085	2474	3262	aadA5	0/0	100.0	100.0	AF137361:63-852	aadA5 is an aminoglycoside nucleotidyltransferase gene encoded by plasmids transposons and integrons in E. coli K. pneumoniae Kluyvera georgiana P. aeruginosa and E. cloacae	aminoglycoside
contig00005	186223	189372	acrB	0/0	100.0	100.0	U00096.3:484403-481253	Protein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug/proton antiporter.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00023	40178	43291	acrD	0/0	100.0	98.8	AP009048.1:2586250-2589364	AcrD is an aminoglycoside efflux pump expressed in E. coli. Its expression can be induced by indole and is regulated by baeRS and cpxAR.	aminoglycoside
contig00075	5854	8958	acrF	0/0	100.0	100.0	U00096:3415032-3418137	AcrF is a inner membrane transporter similar to AcrB.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00036	601	1263	acrS	0/0	100.0	100.0	U00096:3413465-3412802	AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.	cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00087	5399	6178	APH(3’’)-Ib	0/0	97.0	99.7	AF313472:15593-16397	APH(3’’)-Ib is an aminoglycoside phosphotransferase encoded by plasmids transposons integrative conjugative elements and chromosomes in Enterobacteriaceae and Pseudomonas spp.	aminoglycoside
contig00087	4563	5399	APH(6)-Id	0/0	100.0	99.9	AF024602:3155-3992	APH(6)-Id is an aminoglycoside phosphotransferase encoded by plasmids integrative conjugative elements and chromosomal genomic islands in K. pneumoniae Salmonella spp. E. coli Shigella flexneri Providencia alcalifaciens Pseudomonas spp. V. cholerae Edwardsiella tarda Pasteurella multocida and Aeromonas bestiarum	aminoglycoside
contig00021	70354	71173	bacA	0/0	99.8	98.5	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00050	30161	30883	baeR	0/0	100.0	99.3	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00050	28761	30164	baeS	0/0	100.0	98.7	AP009048:2165012-2166416	BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.	aminocoumarin, aminoglycoside
contig00092	221	880	catI	0/0	100.0	99.8	V00622:243-903	catI is a chromosome and transposon-encoded variant of the cat gene found in Escherichia coli and Acinetobacter baumannii	phenicol
contig00024	61576	62949	cpxA	0/0	100.0	99.0	BA000007.3:4905062-4903688	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	aminocoumarin, aminoglycoside
contig00008	15081	15713	CRP	0/0	100.0	99.7	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00090	1871	2746	CTX-M-15	0/0	100.0	100.0	AY044436:1435-2311	CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family	cephalosporin
contig00085	1870	2343	dfrA17	0/0	100.0	100.0	DQ838665:0-474	dfrA17 is an integron-encoded dihydrofolate reductase found in Escherichia coli	diaminopyrimidine
contig00011	47169	48341	emrA	0/0	100.0	97.9	AP009048:2810082-2811255	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	fluoroquinolone
contig00011	48358	49896	emrB	0/0	100.0	98.6	U00096:2812615-2814154	emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin.	fluoroquinolone
contig00002	178461	179516	emrK	0/0	100.0	98.0	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00011	46512	47042	emrR	0/0	100.0	99.4	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00002	176923	178461	emrY	0/0	100.0	97.7	D78168:1591-3130	emrY is a multidrug transport that moves substrates across the inner membrane of the Gram-negative E. coli. It is a homolog of emrB.	tetracycline
contig00013	67026	68669	eptA	0/0	100.0	99.9	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00005	189395	190588	Escherichia_coli_acrA	0/0	100.0	100.0	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00022	38239	39372	Escherichia_coli_ampC	0/0	100.0	97.3	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00055	25537	26835	Escherichia_coli_ampC1_beta-lactamase	0/0	99.5	96.1	FN649414.1:2765050-2766355	An ampC-like beta-lactamase identified from Escherichia coli.	cephalosporin, penam
contig00005	100099	101256	Escherichia_coli_ampH	0/0	100.0	100.0	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig00054	24485	24817	Escherichia_coli_emrE	0/0	100.0	91.9	Z11877.1:485-818	Member of the small MDR (multidrug resistance) family of transporters, in Escherichia coli this protein provides resistance against a number of positively charged compounds including ethidium bromide and erythromycin, proton-dependent secondary transporter which exchanges protons for compound translocation	macrolide
contig00006	30138	31370	Escherichia_coli_mdfA	0/0	100.0	98.4	JQ394987:0-1233	Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter.	benzalkonium_chloride, rhodamine, tetracycline
contig00002	180040	180654	evgA	0/0	100.0	99.2	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00002	180659	184252	evgS	0/0	100.0	96.8	U00096:2484373-2487967	EvgS is a sensor protein that phosphorylates the regulatory protein EvgA. evgS corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	fluoroquinolone, macrolide, penam, tetracycline
contig00041	1784	2512	gadW	0/0	100.0	94.7	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig00041	592	1416	gadX	0/0	100.0	100.0	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00010	40941	41354	H-NS	0/0	100.0	99.3	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00014	8068	8745	kdpE	0/0	100.0	100.0	U00096.3:721733-721055	kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding.	aminoglycoside
contig00026	23178	23561	marA	0/0	100.0	100.0	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00050	19901	21148	mdtA	0/0	100.0	98.0	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00050	21148	24270	mdtB	0/0	100.0	97.0	U00096:2155262-2158385	MdtB is a transporter that forms a heteromultimer complex with MdtC to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex.	aminocoumarin
contig00050	24271	27348	mdtC	0/0	100.0	97.7	U00096:2158385-2161463	MdtC is a transporter that forms a heteromultimer complex with MdtB to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex. In the absence of MdtB MdtC can form a homomultimer complex that results in a functioning efflux complex with a narrower drug specificity. mdtC corresponds to 3 loci in Pseudomonas aeruginosa PAO1 (gene name: muxC/muxB) and 3 loci in Pseudomonas aeruginosa LESB58.	aminocoumarin
contig00041	6013	7170	mdtE	0/0	100.0	100.0	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00041	2875	5988	mdtF	0/0	100.0	100.0	U00096:3660413-3663527	MdtF is the multidrug inner membrane transporter for the MdtEF-TolC efflux complex.	fluoroquinolone, macrolide, penam
contig00034	18399	19625	mdtG	0/0	100.0	99.4	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00034	28254	29462	mdtH	0/0	100.0	99.9	U00096:1125326-1124117	Multidrug resistance protein MdtH	fluoroquinolone
contig00047	5118	6350	mdtM	0/0	100.0	100.0	U00096.3:4568519-4567286	Multidrug resistance protein MdtM	acridine_dye, fluoroquinolone, lincosamide, nucleoside, phenicol
contig00013	98407	99438	mdtN	0/0	100.0	100.0	AP009048.1:4307588-4306556	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	acridine_dye, nucleoside
contig00013	99438	101489	mdtO	0/0	100.0	100.0	AP009048.1:4306557-4304505	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00013	101486	102952	mdtP	0/0	100.0	99.9	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00082	6027	6932	mphA	0/0	100.0	99.9	D16251.1:2531-1625	The mphA gene encodes for resistance enzyme MPH(2’)-I which preferentially inactivate 14-membered macrolides (e.g.erythromycin telithromycin roxithromycin) over 16-membered macrolides (e.g.tylosin spiramycin). It phosphorylates macrolides at 2’-OH hydroxyl of desosamine sugar of macrolides in a GTP-dependent manner.	macrolide
contig00023	18997	19471	mphB	0/0	99.6	96.2	AE005174.2:3397370-3397847	The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides.	macrolide
contig00001	51374	53122	msbA	0/0	100.0	100.0	U00096.3:966620-968369	MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability.	nitroimidazole
contig00109	577	1407	OXA-1	0/0	100.0	100.0	JN420336.1:2230-1399	OXA-1 is a beta-lactamase found in E. coli	cephalosporin, penam
contig00002	63949	64917	pmrF	0/0	100.0	98.0	U00096:2367070-2368039	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide
contig00085	3809	4648	sul1	0/0	100.0	100.0	JF969163:1053-1893	Sul1 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria. It is linked to other resistance genes of class 1 integrons.	sulfonamide
contig00087	85	900	sul2	0/0	100.0	100.0	AY055428.1:21084-20268	Sul2 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria usually found on small plasmids.	sulfonamide
contig00082	1940	2800	TEM-1	0/0	100.0	99.9	AL513383:161910-162771	TEM-1 is a broad-spectrum beta-lactamase found in many Gram-negative bacteria. Confers resistance to penicillins and first generation cephalosphorins.	cephalosporin, monobactam, penam, penem
contig00096	1065	2270	tet(B)	0/0	100.0	99.8	AB089595:0-1206	Tet(B) is a tetracycline efflux protein expressed in many Gram-negative bacteria. It confers resistance to tetracycline doxycycline and minocycline but not tigecycline.	tetracycline
contig00021	46587	48074	tolC	0/0	100.0	99.9	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan
contig00002	2073	3716	yojI	0/0	100.0	100.0	U00096.3:2308615-2306971	YojI mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. YojI is capable of pumping out microcin molecules. The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI.	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00093	1406	2266	(AGly)aac3-IId	0/0	100.0	99.9	EU022314:1-861	(AGly)aac3-IId	NA
contig00085	2474	3262	(AGly)aadA5	0/0	100.0	100.0	AF137361:64-852	(AGly)aadA5	NA
contig00087	5399	6178	(AGly)strA	0/0	97.0	99.9	AB366441:22458-23261	(AGly)strA	NA
contig00087	4563	5399	(AGly)strB	0/0	100.0	100.0	FJ474091:264-1100	(AGly)strB	NA
contig00055	25537	26835	(Bla)AmpC1_Ecoli	0/0	99.5	96.1	FN649414:2765051-2766355	(Bla)AmpC1_Ecoli	NA
contig00022	38239	39372	(Bla)AmpC2_Ecoli	0/0	100.0	97.3	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00005	100099	101256	(Bla)ampH_Ecoli	0/0	100.0	100.0	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00090	1871	2746	(Bla)blaCTX-M-15	0/0	100.0	100.0	JQ686199:261-1136	(Bla)blaCTX-M-15	NA
contig00109	577	1407	(Bla)blaOXA-1	0/0	100.0	100.0	JQ682867:1-831	(Bla)blaOXA-1	NA
contig00082	1940	2800	(Bla)blaTEM-105	0/0	100.0	99.9	AF516720:215-1075	(Bla)blaTEM-105	NA
contig00014	60155	62056	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100.0	100.0	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA
contig00082	6027	6932	(MLS)mph(A)	0/0	100.0	99.9	DQ445270:1626-2531	(MLS)mph(A)	NA
contig00092	221	880	(Phe)catA1	0/0	100.0	99.8	V00622:244-903	(Phe)catA1	NA
contig00085	3809	4648	(Sul)sul1	0/0	100.0	100.0	AF071413:6700-7539	(Sul)sul1	NA
contig00087	85	900	(Sul)sul2	0/0	100.0	100.0	EU360945:1617-2432	(Sul)sul2	NA
contig00096	1065	2270	(Tet)tetB	0/0	100.0	99.7	AB089594:1-1206	(Tet)tetB	NA
contig00085	1870	2343	(Tmt)dfrA17	0/0	100.0	100.0	AB126604:98-571	(Tmt)dfrA17	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00093	1406	2266	aac(3)-IId	0/0	100.0	100.0	NG_047251.1	aminoglycoside N-acetyltransferase AAC(3)-IId	GENTAMICIN
contig00109	1538	2092	aac(6’)-Ib-D181Y	0/0	100.0	99.8	NG_067946.1	AAC(6’)-Ib family aminoglycoside 6’-N-acetyltransferase	AMIKACIN, KANAMYCIN, TOBRAMYCIN
contig00085	2474	3262	aadA5	0/0	100.0	100.0	NG_047357.1	ANT(3’’)-Ia family aminoglycoside nucleotidyltransferase AadA5	STREPTOMYCIN
contig00087	5399	6178	aph(3’’)-Ib	0/0	94.2	100.0	NG_056002.2	aminoglycoside O-phosphotransferase APH(3’’)-Ib	STREPTOMYCIN
contig00087	4563	5399	aph(6)-Id	0/0	100.0	100.0	NG_047464.1	aminoglycoside O-phosphotransferase APH(6)-Id	STREPTOMYCIN
contig00090	1871	2746	blaCTX-M-15	0/0	100.0	100.0	NG_048935.1	class A extended-spectrum beta-lactamase CTX-M-15	CEPHALOSPORIN
contig00022	38239	39372	blaEC-15	0/0	100.0	98.5	NG_049081.1	class C extended-spectrum beta-lactamase EC-15	CEPHALOSPORIN
contig00109	577	1407	blaOXA-1	0/0	100.0	100.0	NG_049392.1	oxacillin-hydrolyzing class D beta-lactamase OXA-1	CEPHALOSPORIN
contig00082	1940	2800	blaTEM-1	0/0	100.0	100.0	NG_050145.1	class A broad-spectrum beta-lactamase TEM-1	BETA-LACTAM
contig00092	221	880	catA1	0/0	100.0	99.8	NG_047582.1	type A-1 chloramphenicol O-acetyltransferase	CHLORAMPHENICOL
contig00085	1870	2343	dfrA17	0/0	100.0	99.8	NG_047710.1	trimethoprim-resistant dihydrofolate reductase DfrA17	TRIMETHOPRIM
contig00082	6011	6932	mph(A)	1/1	100.0	99.6	NG_047986.1	Mph(A) family macrolide 2’-phosphotransferase	MACROLIDE
contig00085	3809	4648	sul1	0/0	100.0	100.0	NG_048082.1	sulfonamide-resistant dihydropteroate synthase Sul1	SULFONAMIDE
contig00087	85	900	sul2	0/0	100.0	100.0	NG_051852.1	sulfonamide-resistant dihydropteroate synthase Sul2	SULFONAMIDE
contig00096	1065	2270	tet(B)	0/0	100.0	100.0	NG_048163.1	tetracycline efflux MFS transporter Tet(B)	TETRACYCLINE

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00093	1406	2266	AAC3	0/0	100.0	100.0	MEG_64	Drugs:Aminoglycosides:Aminoglycoside_N-acetyltransferases:AAC3	NA
contig00005	189395	190588	ACRA	0/0	100.0	100.0	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00005	186223	189372	ACRB	0/0	100.0	100.0	MEG_401	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRB	NA
contig00023	40178	43291	ACRD	0/0	100.0	98.8	MEG_407	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ACRD	NA
contig00075	5854	8958	ACRF	0/0	100.0	100.0	MEG_409	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRF	NA
contig00036	601	1263	ACRS	0/0	100.0	100.0	MEG_415	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS	NA
contig00005	100099	101256	AMPH	0/0	100.0	100.0	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00085	2474	3262	ANT3-DPRIME	0/0	100.0	100.0	MEG_928	Drugs:Aminoglycosides:Aminoglycoside_O-nucleotidyltransferases:ANT3-DPRIME	NA
contig00087	5399	6178	APH3-DPRIME	0/0	94.2	100.0	MEG_1019	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH3-DPRIME	NA
contig00087	4563	5399	APH6	0/0	100.0	100.0	MEG_1086	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH6	NA
contig00050	5782	7635	ASMA	0/0	100.0	96.8	MEG_1180	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:ASMA	NA
contig00021	70354	71173	BACA	0/0	99.8	98.8	MEG_1189	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00050	30161	30883	BAER	0/0	100.0	99.3	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00050	28761	30164	BAES	0/0	100.0	98.7	MEG_1193	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES	NA
contig00018	67338	68528	BCR	0/0	100.0	99.9	MEG_1210	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR	NA
contig00022	38239	39372	BLAEC	0/0	100.0	98.5	MEG_1282	Drugs:betalactams:Class_C_betalactamases:BLAEC	NA
contig00092	210	880	CATA	0/0	100.0	100.0	MEG_1593	Drugs:Phenicol:Chloramphenicol_acetyltransferases:CATA	NA
contig00024	60881	61579	CPXAR	0/0	100.0	100.0	MEG_2122	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00024	61576	62949	CPXAR	0/0	100.0	100.0	MEG_2121	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00008	15081	15713	CRP	0/0	100.0	99.7	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00129	62	1004	CTX	0/0	100.0	98.2	MEG_2435	Drugs:betalactams:Class_A_betalactamases:CTX	NA
contig00085	1870	2343	DFRA	0/0	100.0	100.0	MEG_2547	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00011	47169	48341	EMRA	0/0	100.0	97.9	MEG_2722	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA	NA
contig00011	48358	49896	EMRB	0/0	100.0	98.6	MEG_2725	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRB	NA
contig00037	43176	44366	EMRD	0/0	100.0	100.0	MEG_2729	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD	NA
contig00002	178461	179624	EMRK	0/0	100.0	98.2	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig00011	46512	47042	EMRR	0/0	100.0	99.4	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00002	176923	178461	EMRY	0/0	100.0	97.7	MEG_2736	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRY	NA
contig00013	67026	68669	EPTA	0/0	100.0	99.9	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig00002	180659	184252	EVGS	0/0	100.0	97.2	MEG_2869	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EVGS	NA
contig00041	1784	2512	GADW	0/0	100.0	100.0	MEG_3081	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig00041	592	1416	GADX	0/0	100.0	100.0	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00010	40941	41354	HNS	0/0	100.0	99.3	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00014	8068	8745	KDPE	0/0	100.0	100.0	MEG_3448	Drugs:Aminoglycosides:Aminoglycoside_efflux_pumps:KDPE	NA
contig00026	23172	23561	MARA	0/0	100.0	100.0	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00026	22724	23158	MARR	0/0	100.0	100.0	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00006	30138	31370	MDFA	0/0	100.0	100.0	MEG_3737	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDFA	NA
contig00050	19901	21148	MDTA	0/0	100.0	98.0	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00050	21148	24270	MDTB	0/0	100.0	97.0	MEG_3747	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTB	NA
contig00050	24271	27348	MDTC	0/0	100.0	97.7	MEG_3749	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTC	NA
contig00041	6013	7170	MDTE	0/0	100.0	100.0	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00041	2875	5988	MDTF	0/0	100.0	100.0	MEG_3752	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTF	NA
contig00034	18399	19625	MDTG	0/0	100.0	100.0	MEG_3753	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig00034	28254	29462	MDTH	0/0	100.0	99.9	MEG_3755	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTH	NA
contig00026	55954	56283	MDTI	0/0	100.0	100.0	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00026	56270	56635	MDTJ	0/0	100.0	99.5	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00012	66257	67630	MDTK	0/0	100.0	100.0	MEG_3759	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:MDTK	NA
contig00047	5118	6350	MDTM	0/0	100.0	100.0	MEG_3761	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTM	NA
contig00013	98407	99438	MDTN	0/0	100.0	100.0	MEG_3763	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN	NA
contig00013	99438	101489	MDTO	0/0	100.0	100.0	MEG_3764	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTO	NA
contig00013	101486	102952	MDTP	0/0	100.0	99.9	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig00082	6011	6932	MPHA	1/1	100.0	99.6	MEG_4030	Drugs:MLS:Macrolide_phosphotransferases:MPHA	NA
contig00023	18997	19471	MPHB	0/0	99.6	96.2	MEG_4033	Drugs:MLS:Macrolide_phosphotransferases:MPHB	NA
contig00001	51374	53122	MSBA	0/0	100.0	100.0	MEG_4061	Drugs:Multi-drug_resistance:Multi-drug_ABC_efflux_pumps:MSBA	NA
contig00054	24485	24817	MVRC	0/0	100.0	91.9	MEG_4103	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MVRC	NA
contig00109	577	1407	OXA	0/0	100.0	100.0	MEG_4980	Drugs:betalactams:Class_D_betalactamases:OXA	NA
contig00014	60155	62056	PBP2	0/0	100.0	100.0	MEG_5400	Drugs:betalactams:Penicillin_binding_protein:PBP2	NA
contig00055	25537	26835	PBP4B	0/0	99.5	96.1	MEG_5409	Drugs:betalactams:Penicillin_binding_protein:PBP4B	NA
contig00002	63949	64917	PMRF	0/0	100.0	98.0	MEG_5801	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF	NA
contig00056	21724	22593	ROBA	0/0	100.0	99.0	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00043	35222	35545	SOXS	0/0	100.0	100.0	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00085	3808	4775	SULI	0/0	100.0	100.0	MEG_6615	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULI	NA
contig00087	85	900	SULII	0/0	100.0	100.0	MEG_6617	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULII	NA
contig00096	1065	2270	TETB	0/0	100.0	100.0	MEG_7052	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETB	NA
contig00002	2073	3716	YOGI	0/0	100.0	100.0	MEG_7842	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:YOGI	NA

ID224

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00049	11072	11932	aac(3)-IId_1	0/0	100.0	99.8	EU022314	aac(3)-IId	Gentamicin, Tobramycin
contig00066	901	1702	aadA2_1	0/0	97.9	99.9	NC_010870	aadA2	Streptomycin
contig00015	65022	65897	blaCTX-M-55_1	0/0	100.0	100.0	DQ810789	blaCTX-M-55	Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig00049	5240	6100	blaTEM-1B_1	0/0	100.0	100.0	AY458016	blaTEM-1B	Amoxicillin, Ampicillin, Cephalothin, Piperacillin, Ticarcillin
contig00068	1422	2081	catA1_1	0/0	100.0	99.8	V00622	catA1	Chloramphenicol
contig00066	6	503	dfrA12_8	0/0	100.0	100.0	AM040708	dfrA12	Trimethoprim
contig00041	30146	31378	mdf(A)_1	0/0	100.0	99.9	Y08743	mdf(A)
contig00066	8341	9262	mph(A)_2	1/1	100.0	99.7	U36578	mph(A)	Erythromycin, Azithromycin, Spiramycin, Telithromycin
contig00066	2180	3046	sul1_5	0/0	100.0	99.9	EU780013	sul1	Sulfamethoxazole
contig00077	800	2005	tet(B)_2	0/0	100.0	100.0	AF326777	tet(B)	Doxycycline, Tetracycline, Minocycline

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00049	11072	11932	AAC(3)-IId	0/0	100	99.8	EU022314.1:0-861	AAC(3)-IId is a plasmid-encoded aminoglycoside acetyltransferase in E. coli	aminoglycoside
contig00066	923	1702	aadA2	0/0	100	99.9	AF156486:5012-5792	aadA2 is an aminoglycoside nucleotidyltransferase gene encoded by plasmids and integrons in K. pneumoniae Salmonella spp. Corynebacterium glutamicum C. freundii and Aeromonas spp.	aminoglycoside
contig00028	40844	43993	acrB	0/0	100	100.0	U00096.3:484403-481253	Protein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug/proton antiporter.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00011	38956	42069	acrD	0/0	100	100.0	AP009048.1:2586250-2589364	AcrD is an aminoglycoside efflux pump expressed in E. coli. Its expression can be induced by indole and is regulated by baeRS and cpxAR.	aminoglycoside
contig00035	3717	4874	acrE	0/0	100	99.9	U00096:3413863-3415021	AcrE is a membrane fusion protein similar to AcrA.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00035	601	3705	acrF	0/0	100	100.0	U00096:3415032-3418137	AcrF is a inner membrane transporter similar to AcrB.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00035	5273	5935	acrS	0/0	100	100.0	U00096:3413465-3412802	AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.	cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00029	66576	67397	bacA	0/0	100	98.7	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00021	57758	58480	baeR	0/0	100	100.0	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00021	56358	57761	baeS	0/0	100	99.9	AP009048:2165012-2166416	BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.	aminocoumarin, aminoglycoside
contig00068	1422	2081	catI	0/0	100	99.8	V00622:243-903	catI is a chromosome and transposon-encoded variant of the cat gene found in Escherichia coli and Acinetobacter baumannii	phenicol
contig00012	61537	62910	cpxA	0/0	100	99.0	BA000007.3:4905062-4903688	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	aminocoumarin, aminoglycoside
contig00006	15924	16556	CRP	0/0	100	99.4	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00015	65022	65897	CTX-M-55	0/0	100	100.0	DQ885477:0-876	CTX-M-55 is a beta-lactamase found in the Enterobacteriaceae family	cephalosporin
contig00066	6	503	dfrA12	0/0	100	100.0	GU585907.1:22103-21605	dfrA12 is an integron-encoded dihydrofolate reductase found in Vibrio cholerae	diaminopyrimidine
contig00002	58458	59630	emrA	0/0	100	100.0	AP009048:2810082-2811255	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	fluoroquinolone
contig00002	59647	61185	emrB	0/0	100	100.0	U00096:2812615-2814154	emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin.	fluoroquinolone
contig00009	121400	122455	emrK	0/0	100	99.9	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00002	57801	58331	emrR	0/0	100	99.8	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00009	119862	121400	emrY	0/0	100	99.9	D78168:1591-3130	emrY is a multidrug transport that moves substrates across the inner membrane of the Gram-negative E. coli. It is a homolog of emrB.	tetracycline
contig00016	99937	101580	eptA	0/0	100	99.9	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00028	39628	40821	Escherichia_coli_acrA	0/0	100	100.0	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00016	65396	66529	Escherichia_coli_ampC	0/0	100	97.3	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00011	73468	74772	Escherichia_coli_ampC1_beta-lactamase	0/0	100	99.9	FN649414.1:2765050-2766355	An ampC-like beta-lactamase identified from Escherichia coli.	cephalosporin, penam
contig00019	55572	56729	Escherichia_coli_ampH	0/0	100	100.0	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig00041	30146	31378	Escherichia_coli_mdfA	0/0	100	98.4	JQ394987:0-1233	Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter.	benzalkonium_chloride, rhodamine, tetracycline
contig00009	122978	123592	evgA	0/0	100	100.0	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00009	123597	127190	evgS	0/0	100	100.0	U00096:2484373-2487967	EvgS is a sensor protein that phosphorylates the regulatory protein EvgA. evgS corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	fluoroquinolone, macrolide, penam, tetracycline
contig00039	2609	3337	gadW	0/0	100	94.7	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig00039	1418	2242	gadX	0/0	100	100.0	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00030	62969	63382	H-NS	0/0	100	99.3	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00013	8068	8745	kdpE	0/0	100	100.0	U00096.3:721733-721055	kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding.	aminoglycoside
contig00001	230724	231107	marA	0/0	100	100.0	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00021	47498	48745	mdtA	0/0	100	99.8	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00021	48745	51867	mdtB	0/0	100	97.7	U00096:2155262-2158385	MdtB is a transporter that forms a heteromultimer complex with MdtC to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex.	aminocoumarin
contig00021	51868	54945	mdtC	0/0	100	98.4	U00096:2158385-2161463	MdtC is a transporter that forms a heteromultimer complex with MdtB to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex. In the absence of MdtB MdtC can form a homomultimer complex that results in a functioning efflux complex with a narrower drug specificity. mdtC corresponds to 3 loci in Pseudomonas aeruginosa PAO1 (gene name: muxC/muxB) and 3 loci in Pseudomonas aeruginosa LESB58.	aminocoumarin
contig00039	6838	7995	mdtE	0/0	100	100.0	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00039	3700	6813	mdtF	0/0	100	100.0	U00096:3660413-3663527	MdtF is the multidrug inner membrane transporter for the MdtEF-TolC efflux complex.	fluoroquinolone, macrolide, penam
contig00018	16915	18141	mdtG	0/0	100	99.4	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00018	26770	27978	mdtH	0/0	100	100.0	U00096:1125326-1124117	Multidrug resistance protein MdtH	fluoroquinolone
contig00031	21875	22906	mdtN	0/0	100	100.0	AP009048.1:4307588-4306556	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	acridine_dye, nucleoside
contig00031	22906	24957	mdtO	0/0	100	100.0	AP009048.1:4306557-4304505	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00031	24954	26420	mdtP	0/0	100	100.0	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00066	8357	9262	mphA	0/0	100	100.0	D16251.1:2531-1625	The mphA gene encodes for resistance enzyme MPH(2’)-I which preferentially inactivate 14-membered macrolides (e.g.erythromycin telithromycin roxithromycin) over 16-membered macrolides (e.g.tylosin spiramycin). It phosphorylates macrolides at 2’-OH hydroxyl of desosamine sugar of macrolides in a GTP-dependent manner.	macrolide
contig00011	17794	18270	mphB	0/0	100	98.3	AE005174.2:3397370-3397847	The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides.	macrolide
contig00004	51432	53180	msbA	0/0	100	100.0	U00096.3:966620-968369	MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability.	nitroimidazole
contig00009	17667	18635	pmrF	0/0	100	100.0	U00096:2367070-2368039	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide
contig00066	2207	3046	sul1	0/0	100	100.0	JF969163:1053-1893	Sul1 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria. It is linked to other resistance genes of class 1 integrons.	sulfonamide
contig00049	5240	6100	TEM-1	0/0	100	99.9	AL513383:161910-162771	TEM-1 is a broad-spectrum beta-lactamase found in many Gram-negative bacteria. Confers resistance to penicillins and first generation cephalosphorins.	cephalosporin, monobactam, penam, penem
contig00077	800	2005	tet(B)	0/0	100	99.8	AB089595:0-1206	Tet(B) is a tetracycline efflux protein expressed in many Gram-negative bacteria. It confers resistance to tetracycline doxycycline and minocycline but not tigecycline.	tetracycline
contig00029	42712	44199	tolC	0/0	100	99.7	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan
contig00037	42508	44151	yojI	0/0	100	100.0	U00096.3:2308615-2306971	YojI mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. YojI is capable of pumping out microcin molecules. The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI.	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00049	11072	11932	(AGly)aac3-IId	0/0	100	99.8	EU022314:1-861	(AGly)aac3-IId	NA
contig00066	923	1702	(AGly)aadA2	0/0	100	99.9	X68227:66-945	(AGly)aadA2	NA
contig00011	73468	74772	(Bla)AmpC1_Ecoli	0/0	100	99.9	FN649414:2765051-2766355	(Bla)AmpC1_Ecoli	NA
contig00016	65396	66529	(Bla)AmpC2_Ecoli	0/0	100	97.3	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00019	55572	56729	(Bla)ampH_Ecoli	0/0	100	100.0	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00015	65022	65897	(Bla)blaCTX-M-55	0/0	100	100.0	HM748991:321-1196	(Bla)blaCTX-M-55	NA
contig00049	5240	6100	(Bla)blaTEM-105	0/0	100	99.9	AF516720:215-1075	(Bla)blaTEM-105	NA
contig00013	60155	62056	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100	100.0	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA
contig00066	8357	9262	(MLS)mph(A)	0/0	100	100.0	DQ445270:1626-2531	(MLS)mph(A)	NA
contig00068	1422	2081	(Phe)catA1	0/0	100	99.8	V00622:244-903	(Phe)catA1	NA
contig00066	2207	3046	(Sul)sul1	0/0	100	100.0	AF071413:6700-7539	(Sul)sul1	NA
contig00077	800	2005	(Tet)tetB	0/0	100	99.7	AB089594:1-1206	(Tet)tetB	NA
contig00066	6	503	(Tmt)dfrA12	0/0	100	100.0	Z21672:310-807	(Tmt)dfrA12	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00049	11072	11932	aac(3)-IId	0/0	100	99.9	NG_047251.1	aminoglycoside N-acetyltransferase AAC(3)-IId	GENTAMICIN
contig00066	911	1702	aadA2	0/0	100	100.0	NG_047343.1	ANT(3’’)-Ia family aminoglycoside nucleotidyltransferase AadA2	STREPTOMYCIN
contig00015	65022	65897	blaCTX-M-55	0/0	100	100.0	NG_049006.1	class A extended-spectrum beta-lactamase CTX-M-55	CEPHALOSPORIN
contig00016	65396	66529	blaEC-15	0/0	100	98.5	NG_049081.1	class C extended-spectrum beta-lactamase EC-15	CEPHALOSPORIN
contig00049	5240	6100	blaTEM-1	0/0	100	100.0	NG_050145.1	class A broad-spectrum beta-lactamase TEM-1	BETA-LACTAM
contig00068	1422	2081	catA1	0/0	100	99.8	NG_047582.1	type A-1 chloramphenicol O-acetyltransferase	CHLORAMPHENICOL
contig00066	6	503	dfrA12	0/0	100	100.0	NG_047689.1	trimethoprim-resistant dihydrofolate reductase DfrA12	TRIMETHOPRIM
contig00066	8341	9262	mph(A)	1/1	100	99.7	NG_047986.1	Mph(A) family macrolide 2’-phosphotransferase	MACROLIDE
contig00066	2207	3046	sul1	0/0	100	100.0	NG_048082.1	sulfonamide-resistant dihydropteroate synthase Sul1	SULFONAMIDE
contig00077	800	2005	tet(B)	0/0	100	100.0	NG_048163.1	tetracycline efflux MFS transporter Tet(B)	TETRACYCLINE

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00049	11072	11932	AAC3	0/0	100.0	99.9	MEG_64	Drugs:Aminoglycosides:Aminoglycoside_N-acetyltransferases:AAC3	NA
contig00028	39628	40821	ACRA	0/0	100.0	100.0	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00028	40844	43993	ACRB	0/0	100.0	100.0	MEG_401	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRB	NA
contig00011	38956	42069	ACRD	0/0	100.0	100.0	MEG_407	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ACRD	NA
contig00035	3717	4874	ACRE	0/0	100.0	99.9	MEG_408	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRE	NA
contig00035	601	3705	ACRF	0/0	100.0	100.0	MEG_409	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRF	NA
contig00035	5273	5935	ACRS	0/0	100.0	100.0	MEG_415	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS	NA
contig00019	55572	56729	AMPH	0/0	100.0	100.0	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00066	901	1702	ANT3-DPRIME	0/0	97.9	99.9	MEG_975	Drugs:Aminoglycosides:Aminoglycoside_O-nucleotidyltransferases:ANT3-DPRIME	NA
contig00021	33306	35158	ASMA	0/0	100.0	97.2	MEG_1180	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:ASMA	NA
contig00029	66576	67397	BACA	0/0	100.0	98.9	MEG_1189	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00021	57758	58480	BAER	0/0	100.0	100.0	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00021	56358	57761	BAES	0/0	100.0	99.9	MEG_1193	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES	NA
contig00014	88265	89455	BCR	0/0	100.0	99.9	MEG_1210	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR	NA
contig00016	65396	66529	BLAEC	0/0	100.0	98.5	MEG_1282	Drugs:betalactams:Class_C_betalactamases:BLAEC	NA
contig00068	1417	2081	CATA	0/0	99.1	100.0	MEG_1593	Drugs:Phenicol:Chloramphenicol_acetyltransferases:CATA	NA
contig00012	60842	61540	CPXAR	0/0	100.0	100.0	MEG_2122	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00012	61537	62910	CPXAR	0/0	100.0	100.0	MEG_2121	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00006	15924	16556	CRP	0/0	100.0	99.4	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00049	14853	15795	CTX	0/0	100.0	98.2	MEG_2435	Drugs:betalactams:Class_A_betalactamases:CTX	NA
contig00066	6	503	DFRA	0/0	100.0	100.0	MEG_2551	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00002	58458	59630	EMRA	0/0	100.0	100.0	MEG_2722	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA	NA
contig00002	59647	61185	EMRB	0/0	100.0	100.0	MEG_2725	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRB	NA
contig00010	87250	88440	EMRD	0/0	100.0	100.0	MEG_2729	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD	NA
contig00009	121400	122563	EMRK	0/0	100.0	99.9	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig00002	57801	58331	EMRR	0/0	100.0	99.8	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00009	119862	121400	EMRY	0/0	100.0	99.9	MEG_2736	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRY	NA
contig00016	99937	101580	EPTA	0/0	100.0	99.9	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig00009	123597	127190	EVGS	0/0	100.0	100.0	MEG_2870	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EVGS	NA
contig00039	2609	3337	GADW	0/0	100.0	100.0	MEG_3081	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig00039	1418	2242	GADX	0/0	100.0	100.0	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00030	62969	63382	HNS	0/0	100.0	99.3	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00013	8068	8745	KDPE	0/0	100.0	100.0	MEG_3448	Drugs:Aminoglycosides:Aminoglycoside_efflux_pumps:KDPE	NA
contig00001	230724	231113	MARA	0/0	100.0	100.0	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00001	231127	231561	MARR	0/0	100.0	100.0	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00041	30146	31378	MDFA	0/0	100.0	100.0	MEG_3737	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDFA	NA
contig00021	47498	48745	MDTA	0/0	100.0	99.8	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00021	48745	51867	MDTB	0/0	100.0	97.7	MEG_3747	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTB	NA
contig00021	51868	54945	MDTC	0/0	100.0	98.4	MEG_3749	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTC	NA
contig00039	6838	7995	MDTE	0/0	100.0	100.0	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00039	3700	6813	MDTF	0/0	100.0	100.0	MEG_3752	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTF	NA
contig00018	16915	18141	MDTG	0/0	100.0	100.0	MEG_3753	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig00018	26770	27978	MDTH	0/0	100.0	100.0	MEG_3755	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTH	NA
contig00001	198002	198331	MDTI	0/0	100.0	100.0	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00001	197650	198015	MDTJ	0/0	100.0	99.5	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00001	126248	127621	MDTK	0/0	100.0	99.9	MEG_3759	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:MDTK	NA
contig00031	21875	22906	MDTN	0/0	100.0	100.0	MEG_3763	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN	NA
contig00031	22906	24957	MDTO	0/0	100.0	100.0	MEG_3764	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTO	NA
contig00031	24954	26420	MDTP	0/0	100.0	100.0	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig00066	8341	9262	MPHA	1/1	100.0	99.7	MEG_4030	Drugs:MLS:Macrolide_phosphotransferases:MPHA	NA
contig00011	17794	18270	MPHB	0/0	100.0	98.3	MEG_4033	Drugs:MLS:Macrolide_phosphotransferases:MPHB	NA
contig00004	51432	53180	MSBA	0/0	100.0	100.0	MEG_4061	Drugs:Multi-drug_resistance:Multi-drug_ABC_efflux_pumps:MSBA	NA
contig00013	60155	62056	PBP2	0/0	100.0	100.0	MEG_5400	Drugs:betalactams:Penicillin_binding_protein:PBP2	NA
contig00011	73468	74772	PBP4B	0/0	100.0	99.9	MEG_5409	Drugs:betalactams:Penicillin_binding_protein:PBP4B	NA
contig00009	17667	18635	PMRF	0/0	100.0	100.0	MEG_5801	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF	NA
contig00003	58511	59380	ROBA	0/0	100.0	99.0	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00031	48037	48360	SOXS	0/0	100.0	100.0	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00066	2206	3173	SULI	0/0	100.0	100.0	MEG_6615	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULI	NA
contig00077	800	2005	TETB	0/0	100.0	100.0	MEG_7052	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETB	NA
contig00077	2799	3215	TETD	0/0	100.0	100.0	MEG_7070	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETD	NA
contig00037	42508	44151	YOGI	0/0	100.0	100.0	MEG_7842	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:YOGI	NA

ID228

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00075	1696	2556	aac(3)-IIa_1	0/0	100.0	99.8	X51534	aac(3)-IIa	Gentamicin, Tobramycin
contig00087	1539	2138	aac(6’)-Ib-cr_1	0/0	100.0	100.0	DQ303918	aac(6’)-Ib-cr	Ciprofloxacin
contig00055	1303	2091	aadA5_1	0/0	100.0	100.0	AF137361	aadA5	Streptomycin
contig00072	970	1773	aph(3’’)-Ib_5	0/0	100.0	100.0	AF321551	aph(3’’)-Ib	Streptomycin
contig00072	134	970	aph(6)-Id_1	0/0	100.0	99.9	M28829	aph(6)-Id	Streptomycin
contig00076	1615	2490	blaCTX-M-15_1	0/0	100.0	100.0	AY044436	blaCTX-M-15	Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig00087	578	1408	blaOXA-1_1	0/0	100.0	100.0	HQ170510	blaOXA-1	Amoxicillin, Amoxicillin+Clavulanic_acid, Ampicillin, Ampicillin+Clavulanic_acid, Cefepime, Piperacillin, Piperacillin+Tazobactam
contig00041	14379	15239	blaTEM-1B_1	0/0	100.0	100.0	AY458016	blaTEM-1B	Amoxicillin, Ampicillin, Cephalothin, Piperacillin, Ticarcillin
contig00055	699	1172	dfrA17_1	0/0	100.0	100.0	FJ460238	dfrA17	Trimethoprim
contig00002	64083	65315	mdf(A)_1	0/0	100.0	97.8	Y08743	mdf(A)
contig00104	68	989	mph(A)_2	1/1	100.0	99.6	U36578	mph(A)	Erythromycin, Azithromycin, Spiramycin, Telithromycin
contig00055	2611	3477	sul1_5	0/0	100.0	99.9	EU780013	sul1	Sulfamethoxazole
contig00072	1834	2649	sul2_2	0/0	100.0	100.0	AY034138	sul2	Sulfamethoxazole
contig00050	5808	7054	tet(A)_6	0/0	97.8	100.0	AF534183	tet(A)	Doxycycline, Tetracycline

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00075	1696	2556	AAC(3)-IIe	0/0	100.0	99.5	EU022315.1:0-861	AAC(3)-IIe is a plasmid-encoded aminoglycoside acetyltransferase in E. coli	aminoglycoside
contig00087	1539	2138	AAC(6’)-Ib-cr	0/0	100.0	100.0	DQ303918:0-600	AAC(6’)-Ib-cr is an aminoglycoside acetyltransferase encoded by plasmids transposons integrons in Enterobacteriaceae. The aac(6’)-Ib-cr variant gene can induce resistance against aminoglycoside and fluoroquinolone simultaneously	aminoglycoside, fluoroquinolone
contig00055	1303	2091	aadA5	0/0	100.0	100.0	AF137361:63-852	aadA5 is an aminoglycoside nucleotidyltransferase gene encoded by plasmids transposons and integrons in E. coli K. pneumoniae Kluyvera georgiana P. aeruginosa and E. cloacae	aminoglycoside
contig00003	66086	69235	acrB	0/0	100.0	98.8	U00096.3:484403-481253	Protein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug/proton antiporter.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00001	127067	130180	acrD	0/0	100.0	98.7	AP009048.1:2586250-2589364	AcrD is an aminoglycoside efflux pump expressed in E. coli. Its expression can be induced by indole and is regulated by baeRS and cpxAR.	aminoglycoside
contig00012	149301	150458	acrE	0/0	100.0	98.7	U00096:3413863-3415021	AcrE is a membrane fusion protein similar to AcrA.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00012	150470	153574	acrF	0/0	100.0	96.6	U00096:3415032-3418137	AcrF is a inner membrane transporter similar to AcrB.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00012	148240	148902	acrS	0/0	100.0	98.3	U00096:3413465-3412802	AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.	cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00072	970	1773	APH(3’’)-Ib	0/0	100.0	99.8	AF313472:15593-16397	APH(3’’)-Ib is an aminoglycoside phosphotransferase encoded by plasmids transposons integrative conjugative elements and chromosomes in Enterobacteriaceae and Pseudomonas spp.	aminoglycoside
contig00072	134	970	APH(6)-Id	0/0	100.0	99.8	AF024602:3155-3992	APH(6)-Id is an aminoglycoside phosphotransferase encoded by plasmids integrative conjugative elements and chromosomal genomic islands in K. pneumoniae Salmonella spp. E. coli Shigella flexneri Providencia alcalifaciens Pseudomonas spp. V. cholerae Edwardsiella tarda Pasteurella multocida and Aeromonas bestiarum	aminoglycoside
contig00007	52237	53056	bacA	0/0	99.8	98.3	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00001	566512	567233	baeR	0/0	99.9	97.1	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00001	567230	568633	baeS	0/0	100.0	90.5	AP009048:2165012-2166416	BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.	aminocoumarin, aminoglycoside
contig00016	66690	68057	cpxA	0/0	99.6	98.5	BA000007.3:4905062-4903688	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	aminocoumarin, aminoglycoside
contig00008	15089	15721	CRP	0/0	100.0	99.2	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00076	1615	2490	CTX-M-15	0/0	100.0	100.0	AY044436:1435-2311	CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family	cephalosporin
contig00055	699	1172	dfrA17	0/0	100.0	100.0	DQ838665:0-474	dfrA17 is an integron-encoded dihydrofolate reductase found in Escherichia coli	diaminopyrimidine
contig00022	60267	61439	emrA	0/0	100.0	98.0	AP009048:2810082-2811255	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	fluoroquinolone
contig00022	61456	62994	emrB	0/0	100.0	98.4	U00096:2812615-2814154	emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin.	fluoroquinolone
contig00001	222895	223950	emrK	0/0	100.0	97.7	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00022	59610	60140	emrR	0/0	100.0	98.5	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00001	223950	225488	emrY	0/0	100.0	97.7	D78168:1591-3130	emrY is a multidrug transport that moves substrates across the inner membrane of the Gram-negative E. coli. It is a homolog of emrB.	tetracycline
contig00009	146391	148034	eptA	0/0	100.0	91.4	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00003	64870	66063	Escherichia_coli_acrA	0/0	100.0	99.1	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00019	48091	49224	Escherichia_coli_ampC	0/0	100.0	97.8	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00003	153985	155142	Escherichia_coli_ampH	0/0	100.0	97.1	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig00013	28735	29067	Escherichia_coli_emrE	0/0	100.0	92.2	Z11877.1:485-818	Member of the small MDR (multidrug resistance) family of transporters, in Escherichia coli this protein provides resistance against a number of positively charged compounds including ethidium bromide and erythromycin, proton-dependent secondary transporter which exchanges protons for compound translocation	macrolide
contig00002	64083	65315	Escherichia_coli_mdfA	0/0	100.0	96.3	JQ394987:0-1233	Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter.	benzalkonium_chloride, rhodamine, tetracycline
contig00001	221757	222371	evgA	0/0	100.0	99.0	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00001	218159	221752	evgS	0/0	100.0	96.3	U00096:2484373-2487967	EvgS is a sensor protein that phosphorylates the regulatory protein EvgA. evgS corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	fluoroquinolone, macrolide, penam, tetracycline
contig00008	188688	189416	gadW	0/0	100.0	100.0	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig00008	189785	190609	gadX	0/0	100.0	93.9	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00027	39527	39940	H-NS	0/0	100.0	99.3	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00002	219436	220108	kdpE	0/0	99.3	95.5	U00096.3:721733-721055	kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding.	aminoglycoside
contig00004	289457	289840	marA	0/0	100.0	99.0	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00001	576246	577493	mdtA	0/0	100.0	95.6	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00001	573124	576246	mdtB	0/0	100.0	96.2	U00096:2155262-2158385	MdtB is a transporter that forms a heteromultimer complex with MdtC to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex.	aminocoumarin
contig00001	570046	573123	mdtC	0/0	100.0	94.0	U00096:2158385-2161463	MdtC is a transporter that forms a heteromultimer complex with MdtB to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex. In the absence of MdtB MdtC can form a homomultimer complex that results in a functioning efflux complex with a narrower drug specificity. mdtC corresponds to 3 loci in Pseudomonas aeruginosa PAO1 (gene name: muxC/muxB) and 3 loci in Pseudomonas aeruginosa LESB58.	aminocoumarin
contig00008	184030	185187	mdtE	0/0	100.0	98.5	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00008	185212	188325	mdtF	0/0	100.0	97.3	U00096:3660413-3663527	MdtF is the multidrug inner membrane transporter for the MdtEF-TolC efflux complex.	fluoroquinolone, macrolide, penam
contig00011	91826	93052	mdtG	0/0	100.0	98.4	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00011	81989	83197	mdtH	0/0	100.0	98.3	U00096:1125326-1124117	Multidrug resistance protein MdtH	fluoroquinolone
contig00021	38782	40014	mdtM	0/0	100.0	95.0	U00096.3:4568519-4567286	Multidrug resistance protein MdtM	acridine_dye, fluoroquinolone, lincosamide, nucleoside, phenicol
contig00009	116127	117158	mdtN	0/0	100.0	96.2	AP009048.1:4307588-4306556	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	acridine_dye, nucleoside
contig00009	114076	116127	mdtO	0/0	100.0	97.0	AP009048.1:4306557-4304505	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00009	112613	114079	mdtP	0/0	100.0	97.6	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00104	68	973	mphA	0/0	100.0	99.9	D16251.1:2531-1625	The mphA gene encodes for resistance enzyme MPH(2’)-I which preferentially inactivate 14-membered macrolides (e.g.erythromycin telithromycin roxithromycin) over 16-membered macrolides (e.g.tylosin spiramycin). It phosphorylates macrolides at 2’-OH hydroxyl of desosamine sugar of macrolides in a GTP-dependent manner.	macrolide
contig00015	45415	47163	msbA	0/0	100.0	98.1	U00096.3:966620-968369	MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability.	nitroimidazole
contig00087	578	1408	OXA-1	0/0	100.0	100.0	JN420336.1:2230-1399	OXA-1 is a beta-lactamase found in E. coli	cephalosporin, penam
contig00001	332507	333475	pmrF	0/0	100.0	97.6	U00096:2367070-2368039	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide
contig00055	2638	3477	sul1	0/0	100.0	100.0	JF969163:1053-1893	Sul1 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria. It is linked to other resistance genes of class 1 integrons.	sulfonamide
contig00072	1834	2649	sul2	0/0	100.0	100.0	AY055428.1:21084-20268	Sul2 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria usually found on small plasmids.	sulfonamide
contig00041	14379	15239	TEM-1	0/0	100.0	99.9	AL513383:161910-162771	TEM-1 is a broad-spectrum beta-lactamase found in many Gram-negative bacteria. Confers resistance to penicillins and first generation cephalosphorins.	cephalosporin, monobactam, penam, penem
contig00050	5808	7054	tet(A)	0/0	97.8	100.0	AF534183.1:2970-4245	TetA is a tetracycline efflux pump found in many species of Gram-negative bacteria.	tetracycline
contig00007	78739	80226	tolC	0/0	100.0	98.2	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan
contig00001	630589	631755	ugd	0/0	100.0	96.0	U00096:2099613-2098446	PmrE is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin	peptide
contig00001	391680	393323	yojI	0/0	100.0	97.4	U00096.3:2308615-2306971	YojI mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. YojI is capable of pumping out microcin molecules. The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI.	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00075	1696	2556	(AGly)aac3-IIa	0/0	100	99.8	X51534:91-951	(AGly)aac3-IIa	NA
contig00055	1303	2091	(AGly)aadA5	0/0	100	100.0	AF137361:64-852	(AGly)aadA5	NA
contig00072	970	1773	(AGly)strA	0/0	100	99.9	AB366441:22458-23261	(AGly)strA	NA
contig00072	134	970	(AGly)strB	0/0	100	99.9	FJ474091:264-1100	(AGly)strB	NA
contig00019	48091	49224	(Bla)AmpC2_Ecoli	0/0	100	97.8	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00003	153985	155142	(Bla)ampH_Ecoli	0/0	100	97.1	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00076	1615	2490	(Bla)blaCTX-M-15	0/0	100	100.0	JQ686199:261-1136	(Bla)blaCTX-M-15	NA
contig00087	578	1408	(Bla)blaOXA-1	0/0	100	100.0	JQ682867:1-831	(Bla)blaOXA-1	NA
contig00041	14379	15239	(Bla)blaTEM-105	0/0	100	99.9	AF516720:215-1075	(Bla)blaTEM-105	NA
contig00002	278654	280555	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100	98.7	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA
contig00104	68	973	(MLS)mph(A)	0/0	100	99.9	DQ445270:1626-2531	(MLS)mph(A)	NA
contig00055	2638	3477	(Sul)sul1	0/0	100	100.0	AF071413:6700-7539	(Sul)sul1	NA
contig00072	1834	2649	(Sul)sul2	0/0	100	100.0	EU360945:1617-2432	(Sul)sul2	NA
contig00050	5780	7054	(Tet)tetA	0/0	100	100.0	JX424423:94438-95712	(Tet)tetA	NA
contig00050	7085	7735	(Tet)tetR	0/0	100	99.8	HF545434:53576-54226	(Tet)tetR	NA
contig00055	699	1172	(Tmt)dfrA17	0/0	100	100.0	AB126604:98-571	(Tmt)dfrA17	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00075	1696	2556	aac(3)-IIe	0/0	100	99.8	NG_047244.1	aminoglycoside N-acetyltransferase AAC(3)-IIe	GENTAMICIN
contig00087	1539	2093	aac(6’)-Ib-D181Y	0/0	100	99.8	NG_067946.1	AAC(6’)-Ib family aminoglycoside 6’-N-acetyltransferase	AMIKACIN, KANAMYCIN, TOBRAMYCIN
contig00055	1303	2091	aadA5	0/0	100	100.0	NG_047357.1	ANT(3’’)-Ia family aminoglycoside nucleotidyltransferase AadA5	STREPTOMYCIN
contig00072	970	1797	aph(3’’)-Ib	0/0	100	100.0	NG_056002.2	aminoglycoside O-phosphotransferase APH(3’’)-Ib	STREPTOMYCIN
contig00072	134	970	aph(6)-Id	0/0	100	100.0	NG_047466.1	aminoglycoside O-phosphotransferase APH(6)-Id	STREPTOMYCIN
contig00076	1615	2490	blaCTX-M-15	0/0	100	100.0	NG_048935.1	class A extended-spectrum beta-lactamase CTX-M-15	CEPHALOSPORIN
contig00019	48091	49224	blaEC-5	0/0	100	99.5	NG_049085.1	cephalosporin-hydrolyzing class C beta-lactamase EC-5	CEPHALOSPORIN
contig00087	578	1408	blaOXA-1	0/0	100	100.0	NG_049392.1	oxacillin-hydrolyzing class D beta-lactamase OXA-1	CEPHALOSPORIN
contig00041	14379	15239	blaTEM-1	0/0	100	100.0	NG_050145.1	class A broad-spectrum beta-lactamase TEM-1	BETA-LACTAM
contig00055	699	1172	dfrA17	0/0	100	99.8	NG_047710.1	trimethoprim-resistant dihydrofolate reductase DfrA17	TRIMETHOPRIM
contig00104	68	989	mph(A)	1/1	100	99.6	NG_047986.1	Mph(A) family macrolide 2’-phosphotransferase	MACROLIDE
contig00055	2638	3477	sul1	0/0	100	100.0	NG_048082.1	sulfonamide-resistant dihydropteroate synthase Sul1	SULFONAMIDE
contig00072	1834	2649	sul2	0/0	100	100.0	NG_051852.1	sulfonamide-resistant dihydropteroate synthase Sul2	SULFONAMIDE
contig00050	5780	6979	tet(A)	0/0	100	100.0	NG_048154.1	tetracycline efflux MFS transporter Tet(A)	TETRACYCLINE

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00075	1696	2556	AAC3	0/0	100.0	99.8	MEG_44	Drugs:Aminoglycosides:Aminoglycoside_N-acetyltransferases:AAC3	NA
contig00003	64870	66063	ACRA	0/0	100.0	99.1	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00003	66086	69235	ACRB	0/0	100.0	98.8	MEG_401	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRB	NA
contig00001	127067	130180	ACRD	0/0	100.0	98.7	MEG_407	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ACRD	NA
contig00012	149301	150458	ACRE	0/0	100.0	98.7	MEG_408	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRE	NA
contig00012	150470	153574	ACRF	0/0	100.0	96.6	MEG_409	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRF	NA
contig00012	148240	148902	ACRS	0/0	100.0	98.3	MEG_415	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS	NA
contig00003	153985	155142	AMPH	0/0	100.0	97.1	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00055	1303	2091	ANT3-DPRIME	0/0	100.0	100.0	MEG_928	Drugs:Aminoglycosides:Aminoglycoside_O-nucleotidyltransferases:ANT3-DPRIME	NA
contig00072	970	1797	APH3-DPRIME	0/0	100.0	100.0	MEG_1019	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH3-DPRIME	NA
contig00072	134	970	APH6	0/0	100.0	100.0	MEG_1084	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH6	NA
contig00001	589153	591005	ASMA	0/0	100.0	97.6	MEG_1180	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:ASMA	NA
contig00007	52237	53056	BACA	0/0	99.8	98.5	MEG_1189	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00001	566512	567233	BAER	0/0	99.9	97.1	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00001	567230	568633	BAES	0/0	100.0	90.5	MEG_1193	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES	NA
contig00001	416956	418146	BCR	0/0	100.0	96.6	MEG_1210	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR	NA
contig00019	48091	49224	BLAEC	0/0	100.0	99.5	MEG_1275	Drugs:betalactams:Class_C_betalactamases:BLAEC	NA
contig00016	65995	66693	CPXAR	0/0	100.0	98.1	MEG_2118	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00016	66690	68057	CPXAR	0/0	99.6	99.0	MEG_2121	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00008	15089	15721	CRP	0/0	100.0	99.2	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00055	699	1172	DFRA	0/0	100.0	100.0	MEG_2547	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00022	60267	61439	EMRA	0/0	100.0	98.0	MEG_2722	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA	NA
contig00022	61456	62994	EMRB	0/0	100.0	98.4	MEG_2725	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRB	NA
contig00005	194231	195421	EMRD	0/0	100.0	97.5	MEG_2729	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD	NA
contig00001	222787	223950	EMRK	0/0	100.0	97.4	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig00022	59610	60140	EMRR	0/0	100.0	98.5	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00001	223950	225488	EMRY	0/0	100.0	97.7	MEG_2736	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRY	NA
contig00009	146391	148034	EPTA	0/0	100.0	91.4	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig00001	218159	221752	EVGS	0/0	100.0	97.4	MEG_2869	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EVGS	NA
contig00008	188688	189416	GADW	0/0	100.0	100.0	MEG_3082	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig00008	189785	190609	GADX	0/0	100.0	93.9	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00027	39527	39940	HNS	0/0	100.0	99.3	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00002	219436	220108	KDPE	0/0	99.3	95.5	MEG_3448	Drugs:Aminoglycosides:Aminoglycoside_efflux_pumps:KDPE	NA
contig00004	289457	289846	MARA	0/0	100.0	99.0	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00004	289861	290295	MARR	0/0	100.0	98.2	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00002	64083	65315	MDFA	0/0	100.0	97.9	MEG_3737	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDFA	NA
contig00001	576246	577493	MDTA	0/0	100.0	95.6	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00001	573124	576246	MDTB	0/0	100.0	96.2	MEG_3747	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTB	NA
contig00001	570046	573123	MDTC	0/0	100.0	94.0	MEG_3749	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTC	NA
contig00008	184030	185187	MDTE	0/0	100.0	98.5	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00008	185212	188325	MDTF	0/0	100.0	97.3	MEG_3752	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTF	NA
contig00011	91826	93052	MDTG	0/0	100.0	98.5	MEG_3753	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig00011	81989	83197	MDTH	0/0	100.0	98.3	MEG_3755	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTH	NA
contig00004	258563	258892	MDTI	0/0	100.0	98.8	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00004	258211	258576	MDTJ	0/0	100.0	98.4	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00004	191249	192621	MDTK	0/0	99.9	97.7	MEG_3759	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:MDTK	NA
contig00021	38782	40014	MDTM	0/0	100.0	95.0	MEG_3761	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTM	NA
contig00009	116127	117158	MDTN	0/0	100.0	96.2	MEG_3763	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN	NA
contig00009	114076	116127	MDTO	0/0	100.0	97.0	MEG_3764	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTO	NA
contig00009	112613	114079	MDTP	0/0	100.0	97.6	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig00104	68	989	MPHA	1/1	100.0	99.6	MEG_4030	Drugs:MLS:Macrolide_phosphotransferases:MPHA	NA
contig00015	45415	47163	MSBA	0/0	100.0	98.1	MEG_4061	Drugs:Multi-drug_resistance:Multi-drug_ABC_efflux_pumps:MSBA	NA
contig00013	28735	29067	MVRC	0/0	100.0	92.2	MEG_4103	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MVRC	NA
contig00087	578	1408	OXA	0/0	100.0	100.0	MEG_4980	Drugs:betalactams:Class_D_betalactamases:OXA	NA
contig00002	278654	280555	PBP2	0/0	100.0	98.7	MEG_5400	Drugs:betalactams:Penicillin_binding_protein:PBP2	NA
contig00001	332507	333475	PMRF	0/0	100.0	97.6	MEG_5801	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF	NA
contig00006	19703	20572	ROBA	0/0	100.0	99.0	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00009	84260	84582	SOXS	0/0	99.7	98.1	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00055	2637	3604	SULI	0/0	100.0	100.0	MEG_6615	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULI	NA
contig00072	1834	2649	SULII	0/0	100.0	100.0	MEG_6617	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULII	NA
contig00041	14361	15606	TEM	0/0	98.3	99.4	MEG_6875	Drugs:betalactams:Class_A_betalactamases:TEM	NA
contig00050	5780	7054	TETA	0/0	100.0	100.0	MEG_7024	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETA	NA
contig00001	630589	631755	UGD	0/0	100.0	96.0	MEG_7328	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:UGD	NA
contig00001	391680	393323	YOGI	0/0	100.0	97.4	MEG_7842	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:YOGI	NA

ID229

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00003	231391	232266	blaCTX-M-15_1	0/0	100	100.0	AY044436	blaCTX-M-15	Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig00022	30102	31334	mdf(A)_1	0/0	100	99.1	Y08743	mdf(A)
contig00003	226094	226750	qnrS1_1	0/0	100	100.0	AB187515	qnrS1	Ciprofloxacin

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00011	124682	127831	acrB	0/0	100.0	99.1	U00096.3:484403-481253	Protein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug/proton antiporter.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00006	117709	120822	acrD	0/0	100.0	98.8	AP009048.1:2586250-2589364	AcrD is an aminoglycoside efflux pump expressed in E. coli. Its expression can be induced by indole and is regulated by baeRS and cpxAR.	aminoglycoside
contig00005	270325	271482	acrE	0/0	100.0	99.0	U00096:3413863-3415021	AcrE is a membrane fusion protein similar to AcrA.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00005	271494	274598	acrF	0/0	100.0	99.0	U00096:3415032-3418137	AcrF is a inner membrane transporter similar to AcrB.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00005	269264	269926	acrS	0/0	100.0	98.6	U00096:3413465-3412802	AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.	cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00005	60021	60840	bacA	0/0	99.8	98.7	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00003	277506	278228	baeR	0/0	100.0	99.5	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00003	278225	279628	baeS	0/0	100.0	98.7	AP009048:2165012-2166416	BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.	aminocoumarin, aminoglycoside
contig00027	22569	23942	cpxA	0/0	100.0	98.5	BA000007.3:4905062-4903688	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	aminocoumarin, aminoglycoside
contig00008	15936	16568	CRP	0/0	100.0	99.2	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00003	231391	232266	CTX-M-15	0/0	100.0	100.0	AY044436:1435-2311	CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family	cephalosporin
contig00002	27204	28376	emrA	0/0	100.0	98.2	AP009048:2810082-2811255	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	fluoroquinolone
contig00002	28393	29931	emrB	0/0	100.0	98.5	U00096:2812615-2814154	emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin.	fluoroquinolone
contig00006	25955	27010	emrK	0/0	100.0	98.7	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00002	26547	27077	emrR	0/0	100.0	100.0	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00006	24417	25955	emrY	0/0	100.0	98.8	D78168:1591-3130	emrY is a multidrug transport that moves substrates across the inner membrane of the Gram-negative E. coli. It is a homolog of emrB.	tetracycline
contig00021	18418	20061	eptA	0/0	100.0	99.2	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00011	127854	129047	Escherichia_coli_acrA	0/0	100.0	99.8	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00023	50255	51388	Escherichia_coli_ampC	0/0	100.0	97.2	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00006	85287	86591	Escherichia_coli_ampC1_beta-lactamase	0/0	100.0	98.2	FN649414.1:2765050-2766355	An ampC-like beta-lactamase identified from Escherichia coli.	cephalosporin, penam
contig00011	36338	37495	Escherichia_coli_ampH	0/0	100.0	98.7	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig00010	136225	136557	Escherichia_coli_emrE	0/0	100.0	92.2	Z11877.1:485-818	Member of the small MDR (multidrug resistance) family of transporters, in Escherichia coli this protein provides resistance against a number of positively charged compounds including ethidium bromide and erythromycin, proton-dependent secondary transporter which exchanges protons for compound translocation	macrolide
contig00022	30102	31334	Escherichia_coli_mdfA	0/0	100.0	97.6	JQ394987:0-1233	Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter.	benzalkonium_chloride, rhodamine, tetracycline
contig00006	27534	28148	evgA	0/0	100.0	99.0	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00006	28153	31746	evgS	0/0	100.0	99.5	U00096:2484373-2487967	EvgS is a sensor protein that phosphorylates the regulatory protein EvgA. evgS corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	fluoroquinolone, macrolide, penam, tetracycline
contig00008	191054	191782	gadW	0/0	100.0	94.4	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig00008	192150	192974	gadX	0/0	100.0	97.8	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00001	252998	253411	H-NS	0/0	100.0	99.3	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00012	8235	8907	kdpE	0/0	99.3	97.2	U00096.3:721733-721055	kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding.	aminoglycoside
contig00004	244960	245343	marA	0/0	100.0	99.5	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00003	287241	288488	mdtA	0/0	100.0	98.2	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00003	284119	287241	mdtB	0/0	100.0	98.0	U00096:2155262-2158385	MdtB is a transporter that forms a heteromultimer complex with MdtC to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex.	aminocoumarin
contig00003	281041	284118	mdtC	0/0	100.0	98.0	U00096:2158385-2161463	MdtC is a transporter that forms a heteromultimer complex with MdtB to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex. In the absence of MdtB MdtC can form a homomultimer complex that results in a functioning efflux complex with a narrower drug specificity. mdtC corresponds to 3 loci in Pseudomonas aeruginosa PAO1 (gene name: muxC/muxB) and 3 loci in Pseudomonas aeruginosa LESB58.	aminocoumarin
contig00008	186396	187553	mdtE	0/0	100.0	99.7	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00008	187578	190691	mdtF	0/0	100.0	98.6	U00096:3660413-3663527	MdtF is the multidrug inner membrane transporter for the MdtEF-TolC efflux complex.	fluoroquinolone, macrolide, penam
contig00001	462445	463671	mdtG	0/0	100.0	99.2	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00001	452606	453814	mdtH	0/0	100.0	98.8	U00096:1125326-1124117	Multidrug resistance protein MdtH	fluoroquinolone
contig00018	4259	5290	mdtN	0/0	100.0	98.0	AP009048.1:4307588-4306556	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	acridine_dye, nucleoside
contig00018	5290	7341	mdtO	0/0	100.0	98.8	AP009048.1:4306557-4304505	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00018	7338	8804	mdtP	0/0	100.0	98.2	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00006	142312	142788	mphB	0/0	100.0	98.3	AE005174.2:3397370-3397847	The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides.	macrolide
contig00001	598759	600507	msbA	0/0	100.0	99.0	U00096.3:966620-968369	MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability.	nitroimidazole
contig00003	76806	77774	pmrF	0/0	100.0	99.4	U00096:2367070-2368039	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide
contig00003	226094	226750	QnrS1	0/0	100.0	100.0	DQ485529.1:0-657	QnrS1 is a plasmid-mediated quinolone resistance protein found in Shigella flexneri	fluoroquinolone
contig00005	36175	37662	tolC	0/0	100.0	98.4	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan
contig00003	344414	345580	ugd	0/0	100.0	95.9	U00096:2099613-2098446	PmrE is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin	peptide
contig00003	124793	126436	yojI	0/0	100.0	98.2	U00096.3:2308615-2306971	YojI mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. YojI is capable of pumping out microcin molecules. The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI.	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00006	85287	86591	(Bla)AmpC1_Ecoli	0/0	100	98.2	FN649414:2765051-2766355	(Bla)AmpC1_Ecoli	NA
contig00023	50255	51388	(Bla)AmpC2_Ecoli	0/0	100	97.2	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00011	36338	37495	(Bla)ampH_Ecoli	0/0	100	98.7	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00003	231391	232266	(Bla)blaCTX-M-15	0/0	100	100.0	JQ686199:261-1136	(Bla)blaCTX-M-15	NA
contig00012	60696	62597	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100	98.7	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA
contig00003	226094	226750	(Flq)qnr-S1	0/0	100	100.0	AB187515:9737-10393	(Flq)qnr-S1	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00003	231391	232266	blaCTX-M-15	0/0	100	100.0	NG_048935.1	class A extended-spectrum beta-lactamase CTX-M-15	CEPHALOSPORIN
contig00023	50255	51388	blaEC-13	0/0	100	99.6	NG_049079.1	class C extended-spectrum beta-lactamase EC-13	CEPHALOSPORIN
contig00003	226094	226750	qnrS1	0/0	100	100.0	NG_050543.1	quinolone resistance pentapeptide repeat protein QnrS1	QUINOLONE

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00011	127854	129047	ACRA	0/0	100.0	99.8	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00011	124682	127831	ACRB	0/0	100.0	99.1	MEG_401	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRB	NA
contig00006	117709	120822	ACRD	0/0	100.0	98.8	MEG_407	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ACRD	NA
contig00005	270325	271482	ACRE	0/0	100.0	99.0	MEG_408	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRE	NA
contig00005	271494	274598	ACRF	0/0	100.0	99.0	MEG_409	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRF	NA
contig00005	269264	269926	ACRS	0/0	100.0	98.6	MEG_415	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS	NA
contig00011	36338	37495	AMPH	0/0	100.0	98.7	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00003	300095	301947	ASMA	0/0	100.0	98.1	MEG_1180	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:ASMA	NA
contig00005	60021	60840	BACA	0/0	99.8	98.9	MEG_1189	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00003	277506	278228	BAER	0/0	100.0	99.5	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00003	278225	279628	BAES	0/0	100.0	98.7	MEG_1193	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES	NA
contig00003	151708	152898	BCR	0/0	100.0	98.2	MEG_1210	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR	NA
contig00023	50255	51388	BLAEC	0/0	100.0	99.6	MEG_1280	Drugs:betalactams:Class_C_betalactamases:BLAEC	NA
contig00027	21874	22572	CPXAR	0/0	100.0	99.4	MEG_2118	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00027	22569	23942	CPXAR	0/0	100.0	99.1	MEG_2121	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00008	15936	16568	CRP	0/0	100.0	99.2	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00002	27204	28376	EMRA	0/0	100.0	98.2	MEG_2722	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA	NA
contig00002	28393	29931	EMRB	0/0	100.0	98.5	MEG_2725	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRB	NA
contig00015	27130	28320	EMRD	0/0	100.0	99.9	MEG_2729	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD	NA
contig00006	25955	27118	EMRK	0/0	100.0	98.8	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig00002	26547	27077	EMRR	0/0	100.0	100.0	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00006	24417	25955	EMRY	0/0	100.0	98.9	MEG_2736	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRY	NA
contig00021	18418	20061	EPTA	0/0	100.0	99.2	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig00006	28153	31746	EVGS	0/0	100.0	99.5	MEG_2870	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EVGS	NA
contig00008	191054	191782	GADW	0/0	100.0	98.6	MEG_3081	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig00008	192150	192974	GADX	0/0	100.0	97.8	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00001	252998	253411	HNS	0/0	100.0	99.3	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00012	8235	8907	KDPE	0/0	99.3	97.2	MEG_3448	Drugs:Aminoglycosides:Aminoglycoside_efflux_pumps:KDPE	NA
contig00004	244960	245349	MARA	0/0	100.0	99.5	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00004	245363	245797	MARR	0/0	100.0	97.7	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00022	30102	31334	MDFA	0/0	100.0	99.2	MEG_3737	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDFA	NA
contig00003	287241	288488	MDTA	0/0	100.0	98.2	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00003	284119	287241	MDTB	0/0	100.0	98.0	MEG_3747	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTB	NA
contig00003	281041	284118	MDTC	0/0	100.0	98.0	MEG_3749	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTC	NA
contig00008	186396	187553	MDTE	0/0	100.0	99.7	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00008	187578	190691	MDTF	0/0	100.0	98.6	MEG_3752	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTF	NA
contig00001	462445	463671	MDTG	0/0	100.0	99.3	MEG_3753	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig00001	452606	453814	MDTH	0/0	100.0	98.8	MEG_3755	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTH	NA
contig00004	205985	206314	MDTI	0/0	100.0	99.7	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00004	205633	205998	MDTJ	0/0	100.0	98.9	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00004	134591	135964	MDTK	0/0	100.0	99.0	MEG_3759	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:MDTK	NA
contig00018	4259	5290	MDTN	0/0	100.0	98.0	MEG_3763	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN	NA
contig00018	5290	7341	MDTO	0/0	100.0	98.8	MEG_3764	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTO	NA
contig00018	7338	8804	MDTP	0/0	100.0	98.2	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig00006	142312	142788	MPHB	0/0	100.0	98.3	MEG_4033	Drugs:MLS:Macrolide_phosphotransferases:MPHB	NA
contig00001	598759	600507	MSBA	0/0	100.0	99.0	MEG_4061	Drugs:Multi-drug_resistance:Multi-drug_ABC_efflux_pumps:MSBA	NA
contig00010	136225	136557	MVRC	0/0	100.0	92.2	MEG_4103	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MVRC	NA
contig00012	60696	62597	PBP2	0/0	100.0	98.7	MEG_5400	Drugs:betalactams:Penicillin_binding_protein:PBP2	NA
contig00006	85287	86591	PBP4B	0/0	100.0	98.2	MEG_5409	Drugs:betalactams:Penicillin_binding_protein:PBP4B	NA
contig00003	76806	77774	PMRF	0/0	100.0	99.4	MEG_5801	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF	NA
contig00003	226094	226750	QNRS	0/0	100.0	100.0	MEG_6020	Drugs:Fluoroquinolones:Quinolone_resistance_protein_Qnr:QNRS	NA
contig00013	11905	12774	ROBA	0/0	100.0	99.1	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00018	30421	30743	SOXS	0/0	99.7	99.7	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00003	344414	345580	UGD	0/0	100.0	95.9	MEG_7328	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:UGD	NA
contig00003	124793	126436	YOGI	0/0	100.0	98.2	MEG_7842	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:YOGI	NA

ID231

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00050	1406	2209	aph(3’’)-Ib_5	0/0	100.0	100.0	AF321551	aph(3’’)-Ib	Streptomycin
contig00050	570	1406	aph(6)-Id_1	0/0	100.0	100.0	M28829	aph(6)-Id	Streptomycin
contig00052	1142	2017	blaCTX-M-15_1	0/0	100.0	100.0	AY044436	blaCTX-M-15	Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig00046	3175	4035	blaTEM-1B_1	0/0	100.0	100.0	AY458016	blaTEM-1B	Amoxicillin, Ampicillin, Cephalothin, Piperacillin, Ticarcillin
contig00063	182	664	dfrA14_5	0/0	100.0	99.6	DQ388123	dfrA14	Trimethoprim
contig00022	64607	65839	mdf(A)_1	0/0	100.0	99.1	Y08743	mdf(A)
contig00046	8137	9058	mph(A)_2	1/1	100.0	99.7	U36578	mph(A)	Erythromycin, Azithromycin, Spiramycin, Telithromycin
contig00045	1419	2075	qnrS1_1	0/0	100.0	100.0	AB187515	qnrS1	Ciprofloxacin
contig00050	2270	3085	sul2_2	0/0	100.0	100.0	AY034138	sul2	Sulfamethoxazole
contig00054	2413	3659	tet(A)_6	0/0	97.8	100.0	AF534183	tet(A)	Doxycycline, Tetracycline

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00009	124682	127831	acrB	0/0	100.0	99.1	U00096.3:484403-481253	Protein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug/proton antiporter.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00010	117709	120822	acrD	0/0	100.0	98.8	AP009048.1:2586250-2589364	AcrD is an aminoglycoside efflux pump expressed in E. coli. Its expression can be induced by indole and is regulated by baeRS and cpxAR.	aminoglycoside
contig00003	270324	271481	acrE	0/0	100.0	98.9	U00096:3413863-3415021	AcrE is a membrane fusion protein similar to AcrA.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00003	271493	274597	acrF	0/0	100.0	99.0	U00096:3415032-3418137	AcrF is a inner membrane transporter similar to AcrB.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00003	269263	269925	acrS	0/0	100.0	98.6	U00096:3413465-3412802	AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.	cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00050	1406	2209	APH(3’’)-Ib	0/0	100.0	99.8	AF313472:15593-16397	APH(3’’)-Ib is an aminoglycoside phosphotransferase encoded by plasmids transposons integrative conjugative elements and chromosomes in Enterobacteriaceae and Pseudomonas spp.	aminoglycoside
contig00050	570	1406	APH(6)-Id	0/0	100.0	99.9	AF024602:3155-3992	APH(6)-Id is an aminoglycoside phosphotransferase encoded by plasmids integrative conjugative elements and chromosomal genomic islands in K. pneumoniae Salmonella spp. E. coli Shigella flexneri Providencia alcalifaciens Pseudomonas spp. V. cholerae Edwardsiella tarda Pasteurella multocida and Aeromonas bestiarum	aminoglycoside
contig00003	60020	60839	bacA	0/0	99.8	98.7	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00007	115445	116167	baeR	0/0	100.0	99.5	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00007	114045	115448	baeS	0/0	100.0	98.7	AP009048:2165012-2166416	BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.	aminocoumarin, aminoglycoside
contig00031	22853	24226	cpxA	0/0	100.0	98.5	BA000007.3:4905062-4903688	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	aminocoumarin, aminoglycoside
contig00005	15129	15761	CRP	0/0	100.0	99.2	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00052	1142	2017	CTX-M-15	0/0	100.0	100.0	AY044436:1435-2311	CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family	cephalosporin
contig00063	182	664	dfrA14	0/0	100.0	99.8	EU780012:2162-2645	dfrA14 is an integron-encoded dihydrofolate reductase found in Escherichia coli	diaminopyrimidine
contig00017	43762	44934	emrA	0/0	100.0	98.2	AP009048:2810082-2811255	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	fluoroquinolone
contig00017	42207	43745	emrB	0/0	100.0	98.5	U00096:2812615-2814154	emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin.	fluoroquinolone
contig00010	25955	27010	emrK	0/0	100.0	98.7	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00017	45061	45591	emrR	0/0	100.0	100.0	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00010	24417	25955	emrY	0/0	100.0	98.8	D78168:1591-3130	emrY is a multidrug transport that moves substrates across the inner membrane of the Gram-negative E. coli. It is a homolog of emrB.	tetracycline
contig00029	18403	20046	eptA	0/0	100.0	99.2	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00009	127854	129047	Escherichia_coli_acrA	0/0	100.0	99.8	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00018	92234	93367	Escherichia_coli_ampC	0/0	100.0	97.2	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00010	85287	86591	Escherichia_coli_ampC1_beta-lactamase	0/0	100.0	98.2	FN649414.1:2765050-2766355	An ampC-like beta-lactamase identified from Escherichia coli.	cephalosporin, penam
contig00009	36338	37495	Escherichia_coli_ampH	0/0	100.0	98.7	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig00033	3430	3762	Escherichia_coli_emrE	0/0	100.0	92.5	Z11877.1:485-818	Member of the small MDR (multidrug resistance) family of transporters, in Escherichia coli this protein provides resistance against a number of positively charged compounds including ethidium bromide and erythromycin, proton-dependent secondary transporter which exchanges protons for compound translocation	macrolide
contig00022	64607	65839	Escherichia_coli_mdfA	0/0	100.0	97.6	JQ394987:0-1233	Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter.	benzalkonium_chloride, rhodamine, tetracycline
contig00010	27534	28148	evgA	0/0	100.0	99.0	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00010	28153	31746	evgS	0/0	100.0	99.5	U00096:2484373-2487967	EvgS is a sensor protein that phosphorylates the regulatory protein EvgA. evgS corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	fluoroquinolone, macrolide, penam, tetracycline
contig00005	190175	190903	gadW	0/0	100.0	94.4	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig00005	191271	192095	gadX	0/0	100.0	97.8	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00014	69274	69687	H-NS	0/0	100.0	99.3	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00013	8277	8949	kdpE	0/0	99.3	97.2	U00096.3:721733-721055	kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding.	aminoglycoside
contig00026	52665	53048	marA	0/0	100.0	99.5	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00007	105185	106432	mdtA	0/0	100.0	98.2	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00007	106432	109554	mdtB	0/0	100.0	98.0	U00096:2155262-2158385	MdtB is a transporter that forms a heteromultimer complex with MdtC to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex.	aminocoumarin
contig00007	109555	112632	mdtC	0/0	100.0	98.1	U00096:2158385-2161463	MdtC is a transporter that forms a heteromultimer complex with MdtB to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex. In the absence of MdtB MdtC can form a homomultimer complex that results in a functioning efflux complex with a narrower drug specificity. mdtC corresponds to 3 loci in Pseudomonas aeruginosa PAO1 (gene name: muxC/muxB) and 3 loci in Pseudomonas aeruginosa LESB58.	aminocoumarin
contig00005	185517	186674	mdtE	0/0	100.0	99.7	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00005	186699	189812	mdtF	0/0	100.0	98.6	U00096:3660413-3663527	MdtF is the multidrug inner membrane transporter for the MdtEF-TolC efflux complex.	fluoroquinolone, macrolide, penam
contig00002	198961	200187	mdtG	0/0	100.0	99.2	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00002	208818	210026	mdtH	0/0	100.0	98.8	U00096:1125326-1124117	Multidrug resistance protein MdtH	fluoroquinolone
contig00016	82731	83963	mdtM	0/0	100.0	95.9	U00096.3:4568519-4567286	Multidrug resistance protein MdtM	acridine_dye, fluoroquinolone, lincosamide, nucleoside, phenicol
contig00019	4259	5290	mdtN	0/0	100.0	98.0	AP009048.1:4307588-4306556	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	acridine_dye, nucleoside
contig00019	5290	7341	mdtO	0/0	100.0	98.7	AP009048.1:4306557-4304505	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00019	7338	8804	mdtP	0/0	100.0	98.2	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00046	8153	9058	mphA	0/0	100.0	100.0	D16251.1:2531-1625	The mphA gene encodes for resistance enzyme MPH(2’)-I which preferentially inactivate 14-membered macrolides (e.g.erythromycin telithromycin roxithromycin) over 16-membered macrolides (e.g.tylosin spiramycin). It phosphorylates macrolides at 2’-OH hydroxyl of desosamine sugar of macrolides in a GTP-dependent manner.	macrolide
contig00010	142312	142788	mphB	0/0	100.0	98.3	AE005174.2:3397370-3397847	The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides.	macrolide
contig00002	62125	63873	msbA	0/0	100.0	99.0	U00096.3:966620-968369	MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability.	nitroimidazole
contig00004	124374	125342	pmrF	0/0	100.0	99.4	U00096:2367070-2368039	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide
contig00045	1419	2075	QnrS1	0/0	100.0	100.0	DQ485529.1:0-657	QnrS1 is a plasmid-mediated quinolone resistance protein found in Shigella flexneri	fluoroquinolone
contig00050	2270	3085	sul2	0/0	100.0	100.0	AY055428.1:21084-20268	Sul2 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria usually found on small plasmids.	sulfonamide
contig00046	3175	4035	TEM-1	0/0	100.0	99.9	AL513383:161910-162771	TEM-1 is a broad-spectrum beta-lactamase found in many Gram-negative bacteria. Confers resistance to penicillins and first generation cephalosphorins.	cephalosporin, monobactam, penam, penem
contig00054	2413	3659	tet(A)	0/0	97.8	100.0	AF534183.1:2970-4245	TetA is a tetracycline efflux pump found in many species of Gram-negative bacteria.	tetracycline
contig00003	36175	37662	tolC	0/0	100.0	98.4	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan
contig00004	75712	77355	yojI	0/0	100.0	98.2	U00096.3:2308615-2306971	YojI mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. YojI is capable of pumping out microcin molecules. The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI.	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00050	1406	2209	(AGly)strA	0/0	100	99.9	AB366441:22458-23261	(AGly)strA	NA
contig00050	570	1406	(AGly)strB	0/0	100	100.0	FJ474091:264-1100	(AGly)strB	NA
contig00010	85287	86591	(Bla)AmpC1_Ecoli	0/0	100	98.2	FN649414:2765051-2766355	(Bla)AmpC1_Ecoli	NA
contig00018	92234	93367	(Bla)AmpC2_Ecoli	0/0	100	97.2	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00009	36338	37495	(Bla)ampH_Ecoli	0/0	100	98.7	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00052	1142	2017	(Bla)blaCTX-M-15	0/0	100	100.0	JQ686199:261-1136	(Bla)blaCTX-M-15	NA
contig00046	3175	4035	(Bla)blaTEM-105	0/0	100	99.9	AF516720:215-1075	(Bla)blaTEM-105	NA
contig00013	60738	62639	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100	98.7	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA
contig00045	1419	2075	(Flq)qnr-S1	0/0	100	100.0	AB187515:9737-10393	(Flq)qnr-S1	NA
contig00046	8153	9058	(MLS)mph(A)	0/0	100	100.0	DQ445270:1626-2531	(MLS)mph(A)	NA
contig00050	2270	3085	(Sul)sul2	0/0	100	100.0	EU360945:1617-2432	(Sul)sul2	NA
contig00054	2385	3659	(Tet)tetA	0/0	100	100.0	JX424423:94438-95712	(Tet)tetA	NA
contig00063	182	655	(Tmt)dfrA14	0/0	100	100.0	GU726917:72-545	(Tmt)dfrA14	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00050	1406	2233	aph(3’’)-Ib	0/0	100	100.0	NG_056002.2	aminoglycoside O-phosphotransferase APH(3’’)-Ib	STREPTOMYCIN
contig00050	570	1406	aph(6)-Id	0/0	100	100.0	NG_047464.1	aminoglycoside O-phosphotransferase APH(6)-Id	STREPTOMYCIN
contig00052	1142	2017	blaCTX-M-15	0/0	100	100.0	NG_048935.1	class A extended-spectrum beta-lactamase CTX-M-15	CEPHALOSPORIN
contig00018	92234	93367	blaEC-13	0/0	100	99.6	NG_049079.1	class C extended-spectrum beta-lactamase EC-13	CEPHALOSPORIN
contig00046	3175	4035	blaTEM-1	0/0	100	100.0	NG_050145.1	class A broad-spectrum beta-lactamase TEM-1	BETA-LACTAM
contig00063	182	655	dfrA14	0/0	100	100.0	NG_056035.1	trimethoprim-resistant dihydrofolate reductase DfrA14	TRIMETHOPRIM
contig00046	8137	9058	mph(A)	1/1	100	99.7	NG_047986.1	Mph(A) family macrolide 2’-phosphotransferase	MACROLIDE
contig00045	1419	2075	qnrS1	0/0	100	100.0	NG_050543.1	quinolone resistance pentapeptide repeat protein QnrS1	QUINOLONE
contig00050	2270	3085	sul2	0/0	100	100.0	NG_051852.1	sulfonamide-resistant dihydropteroate synthase Sul2	SULFONAMIDE
contig00054	2385	3584	tet(A)	0/0	100	100.0	NG_048154.1	tetracycline efflux MFS transporter Tet(A)	TETRACYCLINE

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00009	127854	129047	ACRA	0/0	100.0	99.8	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00009	124682	127831	ACRB	0/0	100.0	99.1	MEG_401	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRB	NA
contig00010	117709	120822	ACRD	0/0	100.0	98.8	MEG_407	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ACRD	NA
contig00003	270324	271481	ACRE	0/0	100.0	98.9	MEG_408	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRE	NA
contig00003	271493	274597	ACRF	0/0	100.0	99.0	MEG_409	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRF	NA
contig00003	269263	269925	ACRS	0/0	100.0	98.6	MEG_415	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS	NA
contig00009	36338	37495	AMPH	0/0	100.0	98.7	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00050	1406	2233	APH3-DPRIME	0/0	100.0	100.0	MEG_1019	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH3-DPRIME	NA
contig00050	570	1406	APH6	0/0	100.0	100.0	MEG_1086	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH6	NA
contig00007	90930	92782	ASMA	0/0	100.0	98.0	MEG_1180	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:ASMA	NA
contig00003	60020	60839	BACA	0/0	99.8	98.9	MEG_1189	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00007	115445	116167	BAER	0/0	100.0	99.5	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00007	114045	115448	BAES	0/0	100.0	98.7	MEG_1193	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES	NA
contig00004	49251	50441	BCR	0/0	100.0	98.2	MEG_1210	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR	NA
contig00018	92234	93367	BLAEC	0/0	100.0	99.6	MEG_1280	Drugs:betalactams:Class_C_betalactamases:BLAEC	NA
contig00031	22158	22856	CPXAR	0/0	100.0	99.4	MEG_2118	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00031	22853	24226	CPXAR	0/0	100.0	99.1	MEG_2121	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00005	15129	15761	CRP	0/0	100.0	99.2	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00063	182	655	DFRA	0/0	100.0	99.8	MEG_2517	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00017	43762	44934	EMRA	0/0	100.0	98.2	MEG_2722	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA	NA
contig00017	42207	43745	EMRB	0/0	100.0	98.5	MEG_2725	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRB	NA
contig00006	92098	93288	EMRD	0/0	100.0	99.9	MEG_2729	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD	NA
contig00010	25955	27118	EMRK	0/0	100.0	98.8	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig00017	45061	45591	EMRR	0/0	100.0	100.0	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00010	24417	25955	EMRY	0/0	100.0	98.9	MEG_2736	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRY	NA
contig00029	18403	20046	EPTA	0/0	100.0	99.2	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig00010	28153	31746	EVGS	0/0	100.0	99.5	MEG_2870	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EVGS	NA
contig00005	190175	190903	GADW	0/0	100.0	98.6	MEG_3081	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig00005	191271	192095	GADX	0/0	100.0	97.8	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00014	69274	69687	HNS	0/0	100.0	99.3	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00013	8277	8949	KDPE	0/0	99.3	97.2	MEG_3448	Drugs:Aminoglycosides:Aminoglycoside_efflux_pumps:KDPE	NA
contig00026	52659	53048	MARA	0/0	100.0	99.5	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00026	52211	52645	MARR	0/0	100.0	97.7	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00022	64607	65839	MDFA	0/0	100.0	99.2	MEG_3737	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDFA	NA
contig00007	105185	106432	MDTA	0/0	100.0	98.2	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00007	106432	109554	MDTB	0/0	100.0	98.0	MEG_3747	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTB	NA
contig00007	109555	112632	MDTC	0/0	100.0	98.1	MEG_3749	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTC	NA
contig00005	185517	186674	MDTE	0/0	100.0	99.7	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00005	186699	189812	MDTF	0/0	100.0	98.6	MEG_3752	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTF	NA
contig00002	198961	200187	MDTG	0/0	100.0	99.3	MEG_3753	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig00002	208818	210026	MDTH	0/0	100.0	98.8	MEG_3755	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTH	NA
contig00027	35375	35704	MDTI	0/0	100.0	99.7	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00027	35023	35388	MDTJ	0/0	100.0	98.9	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00008	134590	135963	MDTK	0/0	100.0	99.0	MEG_3759	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:MDTK	NA
contig00016	82731	83963	MDTM	0/0	100.0	95.9	MEG_3761	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTM	NA
contig00019	4259	5290	MDTN	0/0	100.0	98.0	MEG_3763	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN	NA
contig00019	5290	7341	MDTO	0/0	100.0	98.7	MEG_3764	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTO	NA
contig00019	7338	8804	MDTP	0/0	100.0	98.2	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig00046	8137	9058	MPHA	1/1	100.0	99.7	MEG_4030	Drugs:MLS:Macrolide_phosphotransferases:MPHA	NA
contig00010	142312	142788	MPHB	0/0	100.0	98.3	MEG_4033	Drugs:MLS:Macrolide_phosphotransferases:MPHB	NA
contig00002	62125	63873	MSBA	0/0	100.0	99.0	MEG_4061	Drugs:Multi-drug_resistance:Multi-drug_ABC_efflux_pumps:MSBA	NA
contig00033	3430	3762	MVRC	0/0	100.0	92.5	MEG_4103	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MVRC	NA
contig00013	60738	62639	PBP2	0/0	100.0	98.7	MEG_5400	Drugs:betalactams:Penicillin_binding_protein:PBP2	NA
contig00010	85287	86591	PBP4B	0/0	100.0	98.2	MEG_5409	Drugs:betalactams:Penicillin_binding_protein:PBP4B	NA
contig00004	124374	125342	PMRF	0/0	100.0	99.4	MEG_5801	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF	NA
contig00045	1419	2075	QNRS	0/0	100.0	100.0	MEG_6020	Drugs:Fluoroquinolones:Quinolone_resistance_protein_Qnr:QNRS	NA
contig00016	11978	12847	ROBA	0/0	100.0	99.1	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00019	30421	30744	SOXS	0/0	100.0	100.0	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00050	2270	3085	SULII	0/0	100.0	100.0	MEG_6617	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULII	NA
contig00046	3157	4402	TEM	0/0	98.3	99.4	MEG_6875	Drugs:betalactams:Class_A_betalactamases:TEM	NA
contig00054	2385	3659	TETA	0/0	100.0	100.0	MEG_7024	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETA	NA
contig00004	75712	77355	YOGI	0/0	100.0	98.2	MEG_7842	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:YOGI	NA

ID233

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00493	1696	2556	aac(3)-IIa_1	0/0	100	99.8	X51534	aac(3)-IIa	Gentamicin, Tobramycin
contig00886	46	645	aac(6’)-Ib-cr_1	0/0	100	100.0	DQ303918	aac(6’)-Ib-cr	Ciprofloxacin
contig00207	5544	6389	aadA16_1	0/0	100	99.6	EU675686	aadA16	Streptomycin
contig00166	5268	6143	blaCTX-M-15_1	0/0	100	100.0	AY044436	blaCTX-M-15	Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig00676	579	1409	blaOXA-1_1	0/0	100	100.0	HQ170510	blaOXA-1	Amoxicillin, Amoxicillin+Clavulanic_acid, Ampicillin, Ampicillin+Clavulanic_acid, Cefepime, Piperacillin, Piperacillin+Tazobactam
contig00166	1586	2446	blaTEM-1C_1	0/0	100	100.0	FJ560503	blaTEM-1C	Amoxicillin, Ampicillin, Cephalothin, Piperacillin, Ticarcillin
contig00692	89	730	catA2_1	0/0	100	96.1	X53796	catA2	Chloramphenicol
contig00207	6570	7043	dfrA27_1	0/0	100	100.0	FJ459817	dfrA27	Trimethoprim
contig00388	3337	3756	fosA_6	0/0	100	94.0	ACZD01000244	fosA	Fosfomycin
contig00085	5909	7084	oqxA_1	0/0	100	96.0	EU370913	oqxA	Nalidixic_acid, Ciprofloxacin
contig00085	2733	5885	oqxB_1	0/0	100	97.7	EU370913	oqxB	Nalidixic_acid, Ciprofloxacin
contig00207	192	836	qnrB6_2	0/0	100	100.0	EF523819	qnrB6	Ciprofloxacin
contig00207	4247	5113	sul1_5	0/0	100	99.9	EU780013	sul1	Sulfamethoxazole
contig00370	2608	3423	sul2_2	0/0	100	100.0	AY034138	sul2	Sulfamethoxazole

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00493	1696	2556	AAC(3)-IIe	0/0	100.0	99.5	EU022315.1:0-861	AAC(3)-IIe is a plasmid-encoded aminoglycoside acetyltransferase in E. coli	aminoglycoside
contig00886	46	645	AAC(6’)-Ib-cr	0/0	100.0	100.0	DQ303918:0-600	AAC(6’)-Ib-cr is an aminoglycoside acetyltransferase encoded by plasmids transposons integrons in Enterobacteriaceae. The aac(6’)-Ib-cr variant gene can induce resistance against aminoglycoside and fluoroquinolone simultaneously	aminoglycoside, fluoroquinolone
contig00207	5544	6389	aadA16	0/0	100.0	99.6	EU675686:3196-4042	aadA16 is an aminoglycoside nucleotidyltransferase gene encoded by plasmids and integrons in E. coli V. cholerae and K. pneumoniae	aminoglycoside
contig00207	7176	7628	arr-3	0/0	100.0	100.0	EU675686:1956-2409	arr-3 is a plasmid-encoded ribosyltransferase found in Vibrio fluvialis	rifamycin
contig00692	89	730	catII_from_Escherichia_coli_K-12	0/0	100.0	96.1	X53796.1:186-828	catII is a chloramphenicol acetyltransferase. This particular catII is found in E.coli K-12. Confers resistance to chloramphenicol.	phenicol
contig00166	5268	6143	CTX-M-15	0/0	100.0	100.0	AY044436:1435-2311	CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family	cephalosporin
contig00207	6570	7043	dfrA27	0/0	100.0	100.0	KP076293.1:2347-2821	A dihydrofolate reductase and trimethoprim resistance gene from non-O1 non-O139 Vibrio cholerae	diaminopyrimidine
contig00388	3337	3756	FosA5	0/0	100.0	93.3	KP143090.1:1619-1199	fosA5 is a fosfomycin resistance gene isolated from clinical strain of Escherichia coli E265. It is susceptible to amikacin tetracycline and imipenem and resistant to sulphonamide cephalosporins gentamicin ciprofloxacin chloramphenicol and streptomycin	fosfomycin
contig00131	3106	4299	Klebsiella_pneumoniae_acrA	2/3	99.8	94.9	AJ318073.1:793-1990	AcrA is a subunit of the AcrAB multidrug efflux system that in K. pneumoniae which is encoded by the acrRAB operon.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00352	1186	1548	Klebsiella_pneumoniae_KpnE	0/0	100.0	91.7	AP006725.1:2483889-2484252	KpnE subunit of KpnEF resembles EbrAB from E. coli. Mutation in KpnEF resulted in increased susceptibility to cefepime ceftriaxon colistin erythromycin rifampin tetracycline and streptomycin as well as enhanced sensitivity toward sodium dodecyl sulfate deoxycholate dyes benzalkonium chloride chlorhexidine and triclosan	aminoglycoside, cephalosporin, macrolide, peptide, rifamycin, tetracycline
contig00352	870	1199	Klebsiella_pneumoniae_KpnF	0/0	100.0	94.8	AP006725.1:2484238-2484568	KpnF subunit of KpnEF resembles EbrAB from E. coli. Mutation in KpnEF resulted in increased susceptibility to cefepime ceftriaxon colistin erythromycin rifampin tetracycline and streptomycin as well as enhanced sensitivity toward sodium dodecyl sulfate deoxycholate dyes benzalkonium chloride chlorhexidine and triclosan.	aminoglycoside, cephalosporin, macrolide, peptide, rifamycin, tetracycline
contig00341	1038	2162	Klebsiella_pneumoniae_OmpK37	0/0	100.0	95.6	AJ011502.1:300-1425	Klebsiella pneumoniae outer membrane porin protein. Is preferentially detected in porin-deficient strains. Functional characterization of this new porin revealed a narrower pore than those of porins OmpK35 and OmpK36 which did not allow penetration by certain beta-lactams. Also when a resistant strain expresses porin OmpK37 is less susceptible to cefotaxime and cefoxitin than when it is expressing either OmpK36 or OmpK35.	carbapenem, cephalosporin, cephamycin, monobactam, penam, penem
contig00085	5909	7084	oqxA	0/0	100.0	96.0	EU370913.1:46651-47827	RND efflux pump conferring resistance to fluoroquinolone	diaminopyrimidine, fluoroquinolone, glycylcycline, nitrofuran, tetracycline
contig00085	2733	5885	oqxB	0/0	100.0	97.7	EU370913.1:47850-51003	RND efflux pump conferring resistance to fluoroquinolone	diaminopyrimidine, fluoroquinolone, glycylcycline, nitrofuran, tetracycline
contig00676	579	1409	OXA-1	0/0	100.0	100.0	JN420336.1:2230-1399	OXA-1 is a beta-lactamase found in E. coli	cephalosporin, penam
contig00207	156	836	QnrB17	0/0	100.0	99.8	AM919398:0-681	QnrB17 is a plasmid-mediated quinolone resistance protein found in Citrobacter freundii	fluoroquinolone
contig00207	4247	5086	sul1	0/0	100.0	100.0	JF969163:1053-1893	Sul1 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria. It is linked to other resistance genes of class 1 integrons.	sulfonamide
contig00370	2608	3423	sul2	0/0	100.0	100.0	AY055428.1:21084-20268	Sul2 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria usually found on small plasmids.	sulfonamide
contig00166	1586	2446	TEM-1	0/0	100.0	99.9	AL513383:161910-162771	TEM-1 is a broad-spectrum beta-lactamase found in many Gram-negative bacteria. Confers resistance to penicillins and first generation cephalosphorins.	cephalosporin, monobactam, penam, penem

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00493	1696	2556	(AGly)aac3-IIa	0/0	100	99.8	X51534:91-951	(AGly)aac3-IIa	NA
contig00207	5544	6389	(AGly)aadA16	0/0	100	99.6	EU675686:3197-4042	(AGly)aadA16	NA
contig00123	5478	6638	(Bla)ampH	0/0	100	97.8	CP003785:4208384-4209544	(Bla)ampH	NA
contig00166	5268	6143	(Bla)blaCTX-M-15	0/0	100	100.0	JQ686199:261-1136	(Bla)blaCTX-M-15	NA
contig00676	579	1409	(Bla)blaOXA-1	0/0	100	100.0	JQ682867:1-831	(Bla)blaOXA-1	NA
contig00166	1586	2446	(Bla)blaTEM-135	0/0	100	99.9	JQ060998:1-861	(Bla)blaTEM-135	NA
contig00388	3337	3756	(Fcyn)FosA5	0/0	100	93.3	KP143090:1200-1619	(Fcyn)FosA5	NA
contig00085	5909	7084	(Flq)OqxA	0/0	100	96.0	EU370913:46652-47827	(Flq)OqxA	NA
contig00085	2733	5885	(Flq)OqxBgb	0/0	100	97.7	EU370913:47851-51003	(Flq)OqxBgb	NA
contig00207	156	836	(Flq)qnrB17	0/0	100	99.8	AM919398:1-681	(Flq)qnrB17	NA
contig00692	89	730	(Phe)catA2	0/0	100	96.1	X53796:187-903	(Phe)catA2	NA
contig00207	7176	7628	(Rif)arr3	0/0	100	100.0	JF806499:1353-1805	(Rif)arr3	NA
contig00207	4247	5086	(Sul)sul1	0/0	100	100.0	AF071413:6700-7539	(Sul)sul1	NA
contig00370	2608	3423	(Sul)sul2	0/0	100	100.0	EU360945:1617-2432	(Sul)sul2	NA
contig00207	6570	7043	(Tmt)dfrA27	0/0	100	100.0	EU675686:2543-3016	(Tmt)dfrA27	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00493	1696	2556	aac(3)-IIe	0/0	100	99.8	NG_047244.1	aminoglycoside N-acetyltransferase AAC(3)-IIe	GENTAMICIN
contig00886	91	645	aac(6’)-Ib-D181Y	0/0	100	99.8	NG_067946.1	AAC(6’)-Ib family aminoglycoside 6’-N-acetyltransferase	AMIKACIN, KANAMYCIN, TOBRAMYCIN
contig00207	5544	6389	aadA16	0/0	100	100.0	NG_047339.1	ANT(3’’)-Ia family aminoglycoside nucleotidyltransferase AadA16	STREPTOMYCIN
contig00207	7176	7628	arr-3	0/0	100	100.0	NG_048581.1	NAD(+)–rifampin ADP-ribosyltransferase Arr-3	RIFAMYCIN
contig00166	5268	6143	blaCTX-M-15	0/0	100	100.0	NG_048935.1	class A extended-spectrum beta-lactamase CTX-M-15	CEPHALOSPORIN
contig00676	579	1409	blaOXA-1	0/0	100	100.0	NG_049392.1	oxacillin-hydrolyzing class D beta-lactamase OXA-1	CEPHALOSPORIN
contig00166	1586	2446	blaTEM-235	0/0	100	99.9	NG_059898.1	class A beta-lactamase TEM-235	BETA-LACTAM
contig00692	89	730	catA2	0/0	100	100.0	NG_047596.1	type A-2 chloramphenicol O-acetyltransferase CatII	CHLORAMPHENICOL
contig00207	6570	7043	dfrA27	0/0	100	100.0	NG_047723.1	trimethoprim-resistant dihydrofolate reductase DfrA27	TRIMETHOPRIM
contig00388	3337	3756	fosA_gen	0/0	100	94.0	NG_047881.1	FosA family fosfomycin resistance glutathione transferase	FOSFOMYCIN
contig00085	5909	7084	oqxA6	0/0	100	96.3	NG_050424.1	multidrug efflux RND transporter periplasmic adaptor subunit OqxA6	PHENICOL, QUINOLONE
contig00085	2733	5885	oqxB9	0/0	100	99.2	NG_050458.1	multidrug efflux RND transporter permease subunit OqxB9	PHENICOL, QUINOLONE
contig00207	192	836	qnrB6	0/0	100	99.8	NG_050523.1	quinolone resistance pentapeptide repeat protein QnrB6	QUINOLONE
contig00207	4247	5086	sul1	0/0	100	100.0	NG_048082.1	sulfonamide-resistant dihydropteroate synthase Sul1	SULFONAMIDE
contig00370	2608	3423	sul2	0/0	100	100.0	NG_051852.1	sulfonamide-resistant dihydropteroate synthase Sul2	SULFONAMIDE

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00493	1696	2556	AAC3	0/0	100.0	99.8	MEG_44	Drugs:Aminoglycosides:Aminoglycoside_N-acetyltransferases:AAC3	NA
contig00131	3106	4299	ACRA	2/3	99.8	94.9	MEG_400	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00123	5478	6638	AMPH	0/0	100.0	97.8	MEG_730	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00207	5544	6389	ANT3-DPRIME	0/0	100.0	100.0	MEG_763	Drugs:Aminoglycosides:Aminoglycoside_O-nucleotidyltransferases:ANT3-DPRIME	NA
contig00692	89	730	CATA	0/0	100.0	100.0	MEG_1568	Drugs:Phenicol:Chloramphenicol_acetyltransferases:CATA	NA
contig00114	6861	7559	CPXAR	0/0	100.0	97.3	MEG_2116	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00114	7556	8929	CPXAR	0/0	100.0	95.8	MEG_2115	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00001	36024	36966	CTX	0/0	100.0	96.5	MEG_2435	Drugs:betalactams:Class_A_betalactamases:CTX	NA
contig00207	6570	7043	DFRA	0/0	100.0	100.0	MEG_2554	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00388	3337	3756	FOSA	0/0	100.0	94.0	MEG_2991	Drugs:Fosfomycin:Fosfomycin_thiol_transferases:FOSA	NA
contig00110	10041	11272	KDEA	0/0	99.9	94.1	MEG_3447	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:KDEA	NA
contig00352	1186	1548	KPNE	0/0	100.0	91.7	MEG_3514	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:KPNE	NA
contig00352	870	1199	KPNF	0/0	100.0	94.8	MEG_3515	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:KPNF	NA
contig00064	14893	15993	KPNO	2/9	99.7	94.4	MEG_3516	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:KPNO	NA
contig00341	1038	2162	OMP37	0/0	100.0	95.6	MEG_4283	Drugs:betalactams:Mutant_porin_proteins:OMP37	NA
contig00085	5909	7084	OQXA	0/0	100.0	96.3	MEG_4330	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:OQXA	NA
contig00085	2733	5885	OQXB	0/0	100.0	99.2	MEG_4359	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:OQXB	NA
contig00676	579	1409	OXA	0/0	100.0	100.0	MEG_4980	Drugs:betalactams:Class_D_betalactamases:OXA	NA
contig00207	156	836	QNRB	0/0	100.0	100.0	MEG_5999	Drugs:Fluoroquinolones:Quinolone_resistance_protein_Qnr:QNRB	NA
contig00207	4247	5173	SULI	0/0	100.0	100.0	MEG_6616	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULI	NA
contig00370	2608	3423	SULII	0/0	100.0	100.0	MEG_6617	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULII	NA
contig00166	1568	2813	TEM	0/0	98.3	99.6	MEG_6875	Drugs:betalactams:Class_A_betalactamases:TEM	NA

ID235

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00078	1694	2554	aac(3)-IIa_1	0/0	100	99.8	X51534	aac(3)-IIa	Gentamicin, Tobramycin
contig00080	1540	2139	aac(6’)-Ib-cr_1	0/0	100	100.0	DQ303918	aac(6’)-Ib-cr	Ciprofloxacin
contig00057	1443	2231	aadA5_1	0/0	100	100.0	AF137361	aadA5	Streptomycin
contig00063	5421	6200	aph(3’’)-Ib_5	0/0	97	100.0	AF321551	aph(3’’)-Ib	Streptomycin
contig00063	4585	5421	aph(6)-Id_1	0/0	100	100.0	M28829	aph(6)-Id	Streptomycin
contig00016	106674	107549	blaCTX-M-15_1	0/0	100	100.0	AY044436	blaCTX-M-15	Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig00080	579	1409	blaOXA-1_1	0/0	100	100.0	HQ170510	blaOXA-1	Amoxicillin, Amoxicillin+Clavulanic_acid, Ampicillin, Ampicillin+Clavulanic_acid, Cefepime, Piperacillin, Piperacillin+Tazobactam
contig00009	49	909	blaTEM-1B_1	0/0	100	100.0	AY458016	blaTEM-1B	Amoxicillin, Ampicillin, Cephalothin, Piperacillin, Ticarcillin
contig00070	223	882	catA1_1	0/0	100	99.8	V00622	catA1	Chloramphenicol
contig00057	839	1312	dfrA17_1	0/0	100	100.0	FJ460238	dfrA17	Trimethoprim
contig00003	66891	68123	mdf(A)_1	0/0	100	98.3	Y08743	mdf(A)
contig00091	67	988	mph(A)_2	1/1	100	99.7	U36578	mph(A)	Erythromycin, Azithromycin, Spiramycin, Telithromycin
contig00057	2751	3617	sul1_5	0/0	100	99.9	EU780013	sul1	Sulfamethoxazole
contig00063	85	900	sul2_2	0/0	100	100.0	AY034138	sul2	Sulfamethoxazole
contig00073	1131	2336	tet(B)_2	0/0	100	100.0	AF326777	tet(B)	Doxycycline, Tetracycline, Minocycline

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00078	1694	2554	AAC(3)-IIe	0/0	100.0	99.5	EU022315.1:0-861	AAC(3)-IIe is a plasmid-encoded aminoglycoside acetyltransferase in E. coli	aminoglycoside
contig00080	1540	2139	AAC(6’)-Ib-cr	0/0	100.0	100.0	DQ303918:0-600	AAC(6’)-Ib-cr is an aminoglycoside acetyltransferase encoded by plasmids transposons integrons in Enterobacteriaceae. The aac(6’)-Ib-cr variant gene can induce resistance against aminoglycoside and fluoroquinolone simultaneously	aminoglycoside, fluoroquinolone
contig00057	1443	2231	aadA5	0/0	100.0	100.0	AF137361:63-852	aadA5 is an aminoglycoside nucleotidyltransferase gene encoded by plasmids transposons and integrons in E. coli K. pneumoniae Kluyvera georgiana P. aeruginosa and E. cloacae	aminoglycoside
contig00008	118225	121374	acrB	0/0	100.0	99.0	U00096.3:484403-481253	Protein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug/proton antiporter.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00001	339532	342645	acrD	0/0	100.0	98.7	AP009048.1:2586250-2589364	AcrD is an aminoglycoside efflux pump expressed in E. coli. Its expression can be induced by indole and is regulated by baeRS and cpxAR.	aminoglycoside
contig00014	8762	9919	acrE	0/0	100.0	98.2	U00096:3413863-3415021	AcrE is a membrane fusion protein similar to AcrA.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00014	5646	8750	acrF	0/0	100.0	97.5	U00096:3415032-3418137	AcrF is a inner membrane transporter similar to AcrB.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00014	10318	10980	acrS	0/0	100.0	97.6	U00096:3413465-3412802	AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.	cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00063	5421	6200	APH(3’’)-Ib	0/0	97.0	99.7	AF313472:15593-16397	APH(3’’)-Ib is an aminoglycoside phosphotransferase encoded by plasmids transposons integrative conjugative elements and chromosomes in Enterobacteriaceae and Pseudomonas spp.	aminoglycoside
contig00063	4585	5421	APH(6)-Id	0/0	100.0	99.9	AF024602:3155-3992	APH(6)-Id is an aminoglycoside phosphotransferase encoded by plasmids integrative conjugative elements and chromosomal genomic islands in K. pneumoniae Salmonella spp. E. coli Shigella flexneri Providencia alcalifaciens Pseudomonas spp. V. cholerae Edwardsiella tarda Pasteurella multocida and Aeromonas bestiarum	aminoglycoside
contig00005	133326	134145	bacA	0/0	99.8	97.0	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00015	62555	63276	baeR	0/0	99.9	98.1	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00015	63273	64676	baeS	0/0	100.0	96.4	AP009048:2165012-2166416	BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.	aminocoumarin, aminoglycoside
contig00070	223	882	catI	0/0	100.0	99.8	V00622:243-903	catI is a chromosome and transposon-encoded variant of the cat gene found in Escherichia coli and Acinetobacter baumannii	phenicol
contig00019	22665	24038	cpxA	0/0	100.0	98.8	BA000007.3:4905062-4903688	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	aminocoumarin, aminoglycoside
contig00016	15337	15969	CRP	0/0	100.0	99.2	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00016	106674	107549	CTX-M-15	0/0	100.0	100.0	AY044436:1435-2311	CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family	cephalosporin
contig00057	839	1312	dfrA17	0/0	100.0	100.0	DQ838665:0-474	dfrA17 is an integron-encoded dihydrofolate reductase found in Escherichia coli	diaminopyrimidine
contig00004	54759	55931	emrA	0/0	100.0	98.1	AP009048:2810082-2811255	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	fluoroquinolone
contig00004	55948	57486	emrB	0/0	100.0	98.5	U00096:2812615-2814154	emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin.	fluoroquinolone
contig00001	241675	242730	emrK	0/0	100.0	96.9	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00004	54102	54632	emrR	0/0	100.0	99.4	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00001	240137	241675	emrY	0/0	100.0	98.0	D78168:1591-3130	emrY is a multidrug transport that moves substrates across the inner membrane of the Gram-negative E. coli. It is a homolog of emrB.	tetracycline
contig00018	75299	76942	eptA	0/0	100.0	98.2	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00008	121397	122590	Escherichia_coli_acrA	0/0	100.0	99.0	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00006	135097	136230	Escherichia_coli_ampC	0/0	100.0	98.1	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00001	304999	306303	Escherichia_coli_ampC1_beta-lactamase	0/0	100.0	95.2	FN649414.1:2765050-2766355	An ampC-like beta-lactamase identified from Escherichia coli.	cephalosporin, penam
contig00008	30819	31976	Escherichia_coli_ampH	0/0	100.0	97.3	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig00003	66891	68123	Escherichia_coli_mdfA	0/0	100.0	96.8	JQ394987:0-1233	Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter.	benzalkonium_chloride, rhodamine, tetracycline
contig00001	243253	243867	evgA	0/0	100.0	99.3	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00001	243872	247465	evgS	0/0	100.0	96.6	U00096:2484373-2487967	EvgS is a sensor protein that phosphorylates the regulatory protein EvgA. evgS corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	fluoroquinolone, macrolide, penam, tetracycline
contig00009	90677	91405	gadW	0/0	100.0	95.9	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig00009	91774	92598	gadX	0/0	100.0	93.9	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00028	53964	54377	H-NS	0/0	100.0	99.5	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00003	245400	246077	kdpE	0/0	100.0	95.6	U00096.3:721733-721055	kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding.	aminoglycoside
contig00031	27849	28232	marA	0/0	100.0	100.0	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00015	72289	73536	mdtA	0/0	100.0	97.4	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00015	69167	72289	mdtB	0/0	100.0	96.7	U00096:2155262-2158385	MdtB is a transporter that forms a heteromultimer complex with MdtC to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex.	aminocoumarin
contig00015	66089	69166	mdtC	0/0	100.0	97.1	U00096:2158385-2161463	MdtC is a transporter that forms a heteromultimer complex with MdtB to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex. In the absence of MdtB MdtC can form a homomultimer complex that results in a functioning efflux complex with a narrower drug specificity. mdtC corresponds to 3 loci in Pseudomonas aeruginosa PAO1 (gene name: muxC/muxB) and 3 loci in Pseudomonas aeruginosa LESB58.	aminocoumarin
contig00009	86019	87176	mdtE	0/0	100.0	99.0	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00009	87201	90314	mdtF	0/0	100.0	98.4	U00096:3660413-3663527	MdtF is the multidrug inner membrane transporter for the MdtEF-TolC efflux complex.	fluoroquinolone, macrolide, penam
contig00012	152112	153338	mdtG	0/0	100.0	98.3	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00012	142273	143481	mdtH	0/0	100.0	98.0	U00096:1125326-1124117	Multidrug resistance protein MdtH	fluoroquinolone
contig00027	37107	38318	mdtM	0/0	98.3	95.5	U00096.3:4568519-4567286	Multidrug resistance protein MdtM	acridine_dye, fluoroquinolone, lincosamide, nucleoside, phenicol
contig00018	45087	46118	mdtN	0/0	100.0	97.7	AP009048.1:4307588-4306556	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	acridine_dye, nucleoside
contig00018	43036	45087	mdtO	0/0	100.0	96.6	AP009048.1:4306557-4304505	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00018	41573	43039	mdtP	0/0	100.0	96.5	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00091	67	972	mphA	0/0	100.0	100.0	D16251.1:2531-1625	The mphA gene encodes for resistance enzyme MPH(2’)-I which preferentially inactivate 14-membered macrolides (e.g.erythromycin telithromycin roxithromycin) over 16-membered macrolides (e.g.tylosin spiramycin). It phosphorylates macrolides at 2’-OH hydroxyl of desosamine sugar of macrolides in a GTP-dependent manner.	macrolide
contig00001	363352	363826	mphB	0/0	99.6	96.2	AE005174.2:3397370-3397847	The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides.	macrolide
contig00011	51557	53305	msbA	0/0	100.0	98.9	U00096.3:966620-968369	MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability.	nitroimidazole
contig00080	579	1409	OXA-1	0/0	100.0	100.0	JN420336.1:2230-1399	OXA-1 is a beta-lactamase found in E. coli	cephalosporin, penam
contig00001	137295	138263	pmrF	0/0	100.0	97.9	U00096:2367070-2368039	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide
contig00057	2778	3617	sul1	0/0	100.0	100.0	JF969163:1053-1893	Sul1 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria. It is linked to other resistance genes of class 1 integrons.	sulfonamide
contig00063	85	900	sul2	0/0	100.0	100.0	AY055428.1:21084-20268	Sul2 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria usually found on small plasmids.	sulfonamide
contig00009	49	909	TEM-1	0/0	100.0	99.9	AL513383:161910-162771	TEM-1 is a broad-spectrum beta-lactamase found in many Gram-negative bacteria. Confers resistance to penicillins and first generation cephalosphorins.	cephalosporin, monobactam, penam, penem
contig00073	1131	2336	tet(B)	0/0	100.0	99.8	AB089595:0-1206	Tet(B) is a tetracycline efflux protein expressed in many Gram-negative bacteria. It confers resistance to tetracycline doxycycline and minocycline but not tigecycline.	tetracycline
contig00005	111523	113010	tolC	0/0	100.0	97.9	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan
contig00037	22468	23634	ugd	0/0	100.0	96.4	U00096:2099613-2098446	PmrE is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin	peptide
contig00001	75474	77117	yojI	0/0	100.0	97.8	U00096.3:2308615-2306971	YojI mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. YojI is capable of pumping out microcin molecules. The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI.	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00078	1694	2554	(AGly)aac3-IIa	0/0	100	99.8	X51534:91-951	(AGly)aac3-IIa	NA
contig00057	1443	2231	(AGly)aadA5	0/0	100	100.0	AF137361:64-852	(AGly)aadA5	NA
contig00063	5421	6200	(AGly)strA	0/0	97	99.9	AB366441:22458-23261	(AGly)strA	NA
contig00063	4585	5421	(AGly)strB	0/0	100	100.0	FJ474091:264-1100	(AGly)strB	NA
contig00001	304999	306303	(Bla)AmpC1_Ecoli	0/0	100	95.2	FN649414:2765051-2766355	(Bla)AmpC1_Ecoli	NA
contig00006	135097	136230	(Bla)AmpC2_Ecoli	0/0	100	98.1	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00008	30819	31976	(Bla)ampH_Ecoli	0/0	100	97.3	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00016	106674	107549	(Bla)blaCTX-M-15	0/0	100	100.0	JQ686199:261-1136	(Bla)blaCTX-M-15	NA
contig00080	579	1409	(Bla)blaOXA-1	0/0	100	100.0	JQ682867:1-831	(Bla)blaOXA-1	NA
contig00009	49	909	(Bla)blaTEM-105	0/0	100	99.9	AF516720:215-1075	(Bla)blaTEM-105	NA
contig00003	299933	301834	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100	98.4	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA
contig00091	67	972	(MLS)mph(A)	0/0	100	100.0	DQ445270:1626-2531	(MLS)mph(A)	NA
contig00070	223	882	(Phe)catA1	0/0	100	99.8	V00622:244-903	(Phe)catA1	NA
contig00057	2778	3617	(Sul)sul1	0/0	100	100.0	AF071413:6700-7539	(Sul)sul1	NA
contig00063	85	900	(Sul)sul2	0/0	100	100.0	EU360945:1617-2432	(Sul)sul2	NA
contig00073	1131	2336	(Tet)tetB	0/0	100	99.7	AB089594:1-1206	(Tet)tetB	NA
contig00057	839	1312	(Tmt)dfrA17	0/0	100	100.0	AB126604:98-571	(Tmt)dfrA17	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00078	1694	2554	aac(3)-IIe	0/0	100.0	99.8	NG_047244.1	aminoglycoside N-acetyltransferase AAC(3)-IIe	GENTAMICIN
contig00080	1540	2094	aac(6’)-Ib-D181Y	0/0	100.0	99.8	NG_067946.1	AAC(6’)-Ib family aminoglycoside 6’-N-acetyltransferase	AMIKACIN, KANAMYCIN, TOBRAMYCIN
contig00057	1443	2231	aadA5	0/0	100.0	100.0	NG_047357.1	ANT(3’’)-Ia family aminoglycoside nucleotidyltransferase AadA5	STREPTOMYCIN
contig00063	5421	6200	aph(3’’)-Ib	0/0	94.2	100.0	NG_056002.2	aminoglycoside O-phosphotransferase APH(3’’)-Ib	STREPTOMYCIN
contig00063	4585	5421	aph(6)-Id	0/0	100.0	100.0	NG_047464.1	aminoglycoside O-phosphotransferase APH(6)-Id	STREPTOMYCIN
contig00016	106674	107549	blaCTX-M-15	0/0	100.0	100.0	NG_048935.1	class A extended-spectrum beta-lactamase CTX-M-15	CEPHALOSPORIN
contig00006	135097	136230	blaEC-19	0/0	100.0	99.9	NG_049084.1	class C extended-spectrum beta-lactamase EC-19	CEPHALOSPORIN
contig00080	579	1409	blaOXA-1	0/0	100.0	100.0	NG_049392.1	oxacillin-hydrolyzing class D beta-lactamase OXA-1	CEPHALOSPORIN
contig00009	49	909	blaTEM-1	0/0	100.0	100.0	NG_050145.1	class A broad-spectrum beta-lactamase TEM-1	BETA-LACTAM
contig00070	223	882	catA1	0/0	100.0	99.8	NG_047582.1	type A-1 chloramphenicol O-acetyltransferase	CHLORAMPHENICOL
contig00057	839	1312	dfrA17	0/0	100.0	99.8	NG_047710.1	trimethoprim-resistant dihydrofolate reductase DfrA17	TRIMETHOPRIM
contig00091	67	988	mph(A)	1/1	100.0	99.7	NG_047986.1	Mph(A) family macrolide 2’-phosphotransferase	MACROLIDE
contig00057	2778	3617	sul1	0/0	100.0	100.0	NG_048082.1	sulfonamide-resistant dihydropteroate synthase Sul1	SULFONAMIDE
contig00063	85	900	sul2	0/0	100.0	100.0	NG_051852.1	sulfonamide-resistant dihydropteroate synthase Sul2	SULFONAMIDE
contig00073	1131	2336	tet(B)	0/0	100.0	100.0	NG_048163.1	tetracycline efflux MFS transporter Tet(B)	TETRACYCLINE

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00078	1694	2554	AAC3	0/0	100.0	99.8	MEG_44	Drugs:Aminoglycosides:Aminoglycoside_N-acetyltransferases:AAC3	NA
contig00008	121397	122590	ACRA	0/0	100.0	99.0	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00008	118225	121374	ACRB	0/0	100.0	99.0	MEG_401	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRB	NA
contig00001	339532	342645	ACRD	0/0	100.0	98.7	MEG_407	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ACRD	NA
contig00014	8762	9919	ACRE	0/0	100.0	98.2	MEG_408	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRE	NA
contig00014	5646	8750	ACRF	0/0	100.0	97.5	MEG_409	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRF	NA
contig00014	10318	10980	ACRS	0/0	100.0	97.6	MEG_415	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS	NA
contig00008	30819	31976	AMPH	0/0	100.0	97.3	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00057	1443	2231	ANT3-DPRIME	0/0	100.0	100.0	MEG_928	Drugs:Aminoglycosides:Aminoglycoside_O-nucleotidyltransferases:ANT3-DPRIME	NA
contig00063	5421	6200	APH3-DPRIME	0/0	94.2	100.0	MEG_1019	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH3-DPRIME	NA
contig00063	4585	5421	APH6	0/0	100.0	100.0	MEG_1086	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH6	NA
contig00015	85471	87323	ASMA	0/0	100.0	98.3	MEG_1180	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:ASMA	NA
contig00005	133326	134145	BACA	0/0	99.8	97.2	MEG_1189	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00015	62555	63276	BAER	0/0	99.9	98.1	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00015	63273	64676	BAES	0/0	100.0	96.4	MEG_1193	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES	NA
contig00001	49011	50201	BCR	0/0	100.0	96.6	MEG_1210	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR	NA
contig00006	135097	136230	BLAEC	0/0	100.0	99.9	MEG_1277	Drugs:betalactams:Class_C_betalactamases:BLAEC	NA
contig00070	212	882	CATA	0/0	100.0	100.0	MEG_1593	Drugs:Phenicol:Chloramphenicol_acetyltransferases:CATA	NA
contig00019	21970	22668	CPXAR	0/0	100.0	99.4	MEG_2118	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00019	22665	24038	CPXAR	0/0	100.0	99.0	MEG_2121	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00016	15337	15969	CRP	0/0	100.0	99.2	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00057	839	1312	DFRA	0/0	100.0	100.0	MEG_2547	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00004	54759	55931	EMRA	0/0	100.0	98.1	MEG_2722	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA	NA
contig00004	55948	57486	EMRB	0/0	100.0	98.5	MEG_2725	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRB	NA
contig00023	43036	44226	EMRD	0/0	100.0	97.8	MEG_2729	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD	NA
contig00001	241675	242838	EMRK	0/0	100.0	96.7	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig00004	54102	54632	EMRR	0/0	100.0	99.4	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00001	240137	241675	EMRY	0/0	100.0	98.1	MEG_2736	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRY	NA
contig00018	75299	76942	EPTA	0/0	100.0	98.2	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig00001	243872	247465	EVGS	0/0	100.0	97.1	MEG_2869	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EVGS	NA
contig00009	90677	91405	GADW	0/0	100.0	97.0	MEG_3081	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig00009	91774	92598	GADX	0/0	100.0	93.9	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00028	53964	54377	HNS	0/0	100.0	99.5	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00003	245400	246077	KDPE	0/0	100.0	95.6	MEG_3448	Drugs:Aminoglycosides:Aminoglycoside_efflux_pumps:KDPE	NA
contig00031	27843	28232	MARA	0/0	100.0	100.0	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00031	27394	27828	MARR	0/0	100.0	98.6	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00003	66891	68123	MDFA	0/0	100.0	98.4	MEG_3737	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDFA	NA
contig00015	72289	73536	MDTA	0/0	100.0	97.4	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00015	69167	72289	MDTB	0/0	100.0	96.7	MEG_3747	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTB	NA
contig00015	66089	69166	MDTC	0/0	100.0	97.1	MEG_3749	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTC	NA
contig00009	86019	87176	MDTE	0/0	100.0	99.0	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00009	87201	90314	MDTF	0/0	100.0	98.4	MEG_3752	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTF	NA
contig00012	152112	153338	MDTG	0/0	100.0	98.7	MEG_3753	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig00012	142273	143481	MDTH	0/0	100.0	98.0	MEG_3755	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTH	NA
contig00002	326169	326498	MDTI	0/0	100.0	99.7	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00002	325817	326182	MDTJ	0/0	100.0	98.6	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00002	258816	260188	MDTK	0/0	99.9	97.9	MEG_3759	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:MDTK	NA
contig00027	37107	38318	MDTM	0/0	98.3	95.5	MEG_3761	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTM	NA
contig00018	45087	46118	MDTN	0/0	100.0	97.7	MEG_3763	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN	NA
contig00018	43036	45087	MDTO	0/0	100.0	96.6	MEG_3764	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTO	NA
contig00018	41573	43039	MDTP	0/0	100.0	96.5	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig00091	67	988	MPHA	1/1	100.0	99.7	MEG_4030	Drugs:MLS:Macrolide_phosphotransferases:MPHA	NA
contig00001	363352	363826	MPHB	0/0	99.6	96.2	MEG_4033	Drugs:MLS:Macrolide_phosphotransferases:MPHB	NA
contig00011	51557	53305	MSBA	0/0	100.0	98.9	MEG_4061	Drugs:Multi-drug_resistance:Multi-drug_ABC_efflux_pumps:MSBA	NA
contig00080	579	1409	OXA	0/0	100.0	100.0	MEG_4980	Drugs:betalactams:Class_D_betalactamases:OXA	NA
contig00003	299933	301834	PBP2	0/0	100.0	98.4	MEG_5400	Drugs:betalactams:Penicillin_binding_protein:PBP2	NA
contig00001	304999	306303	PBP4B	0/0	100.0	95.2	MEG_5409	Drugs:betalactams:Penicillin_binding_protein:PBP4B	NA
contig00001	137295	138263	PMRF	0/0	100.0	97.9	MEG_5801	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF	NA
contig00029	21728	22597	ROBA	0/0	100.0	98.8	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00018	21050	21372	SOXS	0/0	99.7	97.8	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00057	2777	3744	SULI	0/0	100.0	100.0	MEG_6615	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULI	NA
contig00063	85	900	SULII	0/0	100.0	100.0	MEG_6617	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULII	NA
contig00073	1131	2336	TETB	0/0	100.0	100.0	MEG_7052	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETB	NA
contig00037	22468	23634	UGD	0/0	100.0	96.4	MEG_7328	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:UGD	NA
contig00001	75474	77117	YOGI	0/0	100.0	97.8	MEG_7842	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:YOGI	NA

ID237

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00003	231391	232266	blaCTX-M-15_1	0/0	100	100.0	AY044436	blaCTX-M-15	Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig00022	30105	31337	mdf(A)_1	0/0	100	99.1	Y08743	mdf(A)
contig00003	226094	226750	qnrS1_1	0/0	100	100.0	AB187515	qnrS1	Ciprofloxacin

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00012	125377	128526	acrB	0/0	100.0	99.1	U00096.3:484403-481253	Protein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug/proton antiporter.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00005	117709	120822	acrD	0/0	100.0	98.8	AP009048.1:2586250-2589364	AcrD is an aminoglycoside efflux pump expressed in E. coli. Its expression can be induced by indole and is regulated by baeRS and cpxAR.	aminoglycoside
contig00004	270325	271482	acrE	0/0	100.0	99.0	U00096:3413863-3415021	AcrE is a membrane fusion protein similar to AcrA.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00004	271494	274598	acrF	0/0	100.0	99.0	U00096:3415032-3418137	AcrF is a inner membrane transporter similar to AcrB.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00004	269264	269926	acrS	0/0	100.0	98.6	U00096:3413465-3412802	AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.	cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00004	60021	60840	bacA	0/0	99.8	98.7	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00003	277506	278228	baeR	0/0	100.0	99.5	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00003	278225	279628	baeS	0/0	100.0	98.7	AP009048:2165012-2166416	BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.	aminocoumarin, aminoglycoside
contig00027	22827	24200	cpxA	0/0	100.0	98.5	BA000007.3:4905062-4903688	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	aminocoumarin, aminoglycoside
contig00007	15000	15632	CRP	0/0	100.0	99.2	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00003	231391	232266	CTX-M-15	0/0	100.0	100.0	AY044436:1435-2311	CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family	cephalosporin
contig00002	27204	28376	emrA	0/0	100.0	98.2	AP009048:2810082-2811255	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	fluoroquinolone
contig00002	28393	29931	emrB	0/0	100.0	98.5	U00096:2812615-2814154	emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin.	fluoroquinolone
contig00005	25955	27010	emrK	0/0	100.0	98.7	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00002	26547	27077	emrR	0/0	100.0	100.0	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00005	24417	25955	emrY	0/0	100.0	98.8	D78168:1591-3130	emrY is a multidrug transport that moves substrates across the inner membrane of the Gram-negative E. coli. It is a homolog of emrB.	tetracycline
contig00014	115182	116825	eptA	0/0	100.0	99.2	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00012	128549	129742	Escherichia_coli_acrA	0/0	100.0	99.8	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00024	50255	51388	Escherichia_coli_ampC	0/0	100.0	97.2	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00005	85287	86591	Escherichia_coli_ampC1_beta-lactamase	0/0	100.0	98.2	FN649414.1:2765050-2766355	An ampC-like beta-lactamase identified from Escherichia coli.	cephalosporin, penam
contig00012	37033	38190	Escherichia_coli_ampH	0/0	100.0	98.7	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig00008	136225	136557	Escherichia_coli_emrE	0/0	100.0	92.2	Z11877.1:485-818	Member of the small MDR (multidrug resistance) family of transporters, in Escherichia coli this protein provides resistance against a number of positively charged compounds including ethidium bromide and erythromycin, proton-dependent secondary transporter which exchanges protons for compound translocation	macrolide
contig00022	30105	31337	Escherichia_coli_mdfA	0/0	100.0	97.6	JQ394987:0-1233	Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter.	benzalkonium_chloride, rhodamine, tetracycline
contig00005	27534	28148	evgA	0/0	100.0	99.0	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00005	28153	31746	evgS	0/0	100.0	99.5	U00096:2484373-2487967	EvgS is a sensor protein that phosphorylates the regulatory protein EvgA. evgS corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	fluoroquinolone, macrolide, penam, tetracycline
contig00007	190118	190846	gadW	0/0	100.0	94.4	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig00007	191214	192038	gadX	0/0	100.0	97.8	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00001	226067	226480	H-NS	0/0	100.0	99.3	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00009	8327	8999	kdpE	0/0	99.3	97.2	U00096.3:721733-721055	kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding.	aminoglycoside
contig00015	55320	55703	marA	0/0	100.0	99.5	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00003	287241	288488	mdtA	0/0	100.0	98.2	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00003	284119	287241	mdtB	0/0	100.0	98.0	U00096:2155262-2158385	MdtB is a transporter that forms a heteromultimer complex with MdtC to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex.	aminocoumarin
contig00003	281041	284118	mdtC	0/0	100.0	98.1	U00096:2158385-2161463	MdtC is a transporter that forms a heteromultimer complex with MdtB to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex. In the absence of MdtB MdtC can form a homomultimer complex that results in a functioning efflux complex with a narrower drug specificity. mdtC corresponds to 3 loci in Pseudomonas aeruginosa PAO1 (gene name: muxC/muxB) and 3 loci in Pseudomonas aeruginosa LESB58.	aminocoumarin
contig00007	185460	186617	mdtE	0/0	100.0	99.7	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00007	186642	189755	mdtF	0/0	100.0	98.6	U00096:3660413-3663527	MdtF is the multidrug inner membrane transporter for the MdtEF-TolC efflux complex.	fluoroquinolone, macrolide, penam
contig00001	435515	436741	mdtG	0/0	100.0	99.2	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00001	425676	426884	mdtH	0/0	100.0	98.8	U00096:1125326-1124117	Multidrug resistance protein MdtH	fluoroquinolone
contig00014	91422	92453	mdtN	0/0	100.0	98.0	AP009048.1:4307588-4306556	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	acridine_dye, nucleoside
contig00014	89371	91422	mdtO	0/0	100.0	98.8	AP009048.1:4306557-4304505	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00014	87908	89374	mdtP	0/0	100.0	98.2	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00005	142312	142788	mphB	0/0	100.0	98.3	AE005174.2:3397370-3397847	The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides.	macrolide
contig00010	51631	53379	msbA	0/0	100.0	99.0	U00096.3:966620-968369	MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability.	nitroimidazole
contig00003	76806	77774	pmrF	0/0	100.0	99.4	U00096:2367070-2368039	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide
contig00003	226094	226750	QnrS1	0/0	100.0	100.0	DQ485529.1:0-657	QnrS1 is a plasmid-mediated quinolone resistance protein found in Shigella flexneri	fluoroquinolone
contig00004	36175	37662	tolC	0/0	100.0	98.4	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan
contig00003	344414	345580	ugd	0/0	100.0	95.9	U00096:2099613-2098446	PmrE is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin	peptide
contig00003	124793	126436	yojI	0/0	100.0	98.2	U00096.3:2308615-2306971	YojI mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. YojI is capable of pumping out microcin molecules. The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI.	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00005	85287	86591	(Bla)AmpC1_Ecoli	0/0	100	98.2	FN649414:2765051-2766355	(Bla)AmpC1_Ecoli	NA
contig00024	50255	51388	(Bla)AmpC2_Ecoli	0/0	100	97.2	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00012	37033	38190	(Bla)ampH_Ecoli	0/0	100	98.7	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00003	231391	232266	(Bla)blaCTX-M-15	0/0	100	100.0	JQ686199:261-1136	(Bla)blaCTX-M-15	NA
contig00009	60788	62689	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100	98.7	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA
contig00003	226094	226750	(Flq)qnr-S1	0/0	100	100.0	AB187515:9737-10393	(Flq)qnr-S1	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00003	231391	232266	blaCTX-M-15	0/0	100	100.0	NG_048935.1	class A extended-spectrum beta-lactamase CTX-M-15	CEPHALOSPORIN
contig00024	50255	51388	blaEC-13	0/0	100	99.6	NG_049079.1	class C extended-spectrum beta-lactamase EC-13	CEPHALOSPORIN
contig00003	226094	226750	qnrS1	0/0	100	100.0	NG_050543.1	quinolone resistance pentapeptide repeat protein QnrS1	QUINOLONE

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00012	128549	129742	ACRA	0/0	100.0	99.8	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00012	125377	128526	ACRB	0/0	100.0	99.1	MEG_401	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRB	NA
contig00005	117709	120822	ACRD	0/0	100.0	98.8	MEG_407	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ACRD	NA
contig00004	270325	271482	ACRE	0/0	100.0	99.0	MEG_408	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRE	NA
contig00004	271494	274598	ACRF	0/0	100.0	99.0	MEG_409	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRF	NA
contig00004	269264	269926	ACRS	0/0	100.0	98.6	MEG_415	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS	NA
contig00012	37033	38190	AMPH	0/0	100.0	98.7	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00003	300095	301947	ASMA	0/0	100.0	98.1	MEG_1180	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:ASMA	NA
contig00004	60021	60840	BACA	0/0	99.8	98.9	MEG_1189	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00003	277506	278228	BAER	0/0	100.0	99.5	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00003	278225	279628	BAES	0/0	100.0	98.7	MEG_1193	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES	NA
contig00003	151708	152898	BCR	0/0	100.0	98.2	MEG_1210	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR	NA
contig00024	50255	51388	BLAEC	0/0	100.0	99.6	MEG_1280	Drugs:betalactams:Class_C_betalactamases:BLAEC	NA
contig00027	22132	22830	CPXAR	0/0	100.0	99.4	MEG_2118	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00027	22827	24200	CPXAR	0/0	100.0	99.1	MEG_2121	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00007	15000	15632	CRP	0/0	100.0	99.2	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00002	27204	28376	EMRA	0/0	100.0	98.2	MEG_2722	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA	NA
contig00002	28393	29931	EMRB	0/0	100.0	98.5	MEG_2725	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRB	NA
contig00017	27098	28288	EMRD	0/0	100.0	99.9	MEG_2729	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD	NA
contig00005	25955	27118	EMRK	0/0	100.0	98.8	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig00002	26547	27077	EMRR	0/0	100.0	100.0	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00005	24417	25955	EMRY	0/0	100.0	98.9	MEG_2736	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRY	NA
contig00014	115182	116825	EPTA	0/0	100.0	99.2	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig00005	28153	31746	EVGS	0/0	100.0	99.5	MEG_2870	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EVGS	NA
contig00007	190118	190846	GADW	0/0	100.0	98.6	MEG_3081	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig00007	191214	192038	GADX	0/0	100.0	97.8	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00001	226067	226480	HNS	0/0	100.0	99.3	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00009	8327	8999	KDPE	0/0	99.3	97.2	MEG_3448	Drugs:Aminoglycosides:Aminoglycoside_efflux_pumps:KDPE	NA
contig00015	55314	55703	MARA	0/0	100.0	99.5	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00015	54866	55300	MARR	0/0	100.0	97.7	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00022	30105	31337	MDFA	0/0	100.0	99.2	MEG_3737	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDFA	NA
contig00003	287241	288488	MDTA	0/0	100.0	98.2	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00003	284119	287241	MDTB	0/0	100.0	98.0	MEG_3747	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTB	NA
contig00003	281041	284118	MDTC	0/0	100.0	98.1	MEG_3749	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTC	NA
contig00007	185460	186617	MDTE	0/0	100.0	99.7	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00007	186642	189755	MDTF	0/0	100.0	98.6	MEG_3752	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTF	NA
contig00001	435515	436741	MDTG	0/0	100.0	99.3	MEG_3753	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig00001	425676	426884	MDTH	0/0	100.0	98.8	MEG_3755	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTH	NA
contig00015	94349	94678	MDTI	0/0	100.0	99.7	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00015	94665	95030	MDTJ	0/0	100.0	98.9	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00011	134591	135964	MDTK	0/0	100.0	99.0	MEG_3759	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:MDTK	NA
contig00014	91422	92453	MDTN	0/0	100.0	98.0	MEG_3763	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN	NA
contig00014	89371	91422	MDTO	0/0	100.0	98.8	MEG_3764	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTO	NA
contig00014	87908	89374	MDTP	0/0	100.0	98.2	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig00005	142312	142788	MPHB	0/0	100.0	98.3	MEG_4033	Drugs:MLS:Macrolide_phosphotransferases:MPHB	NA
contig00010	51631	53379	MSBA	0/0	100.0	99.0	MEG_4061	Drugs:Multi-drug_resistance:Multi-drug_ABC_efflux_pumps:MSBA	NA
contig00008	136225	136557	MVRC	0/0	100.0	92.2	MEG_4103	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MVRC	NA
contig00009	60788	62689	PBP2	0/0	100.0	98.7	MEG_5400	Drugs:betalactams:Penicillin_binding_protein:PBP2	NA
contig00005	85287	86591	PBP4B	0/0	100.0	98.2	MEG_5409	Drugs:betalactams:Penicillin_binding_protein:PBP4B	NA
contig00003	76806	77774	PMRF	0/0	100.0	99.4	MEG_5801	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF	NA
contig00003	226094	226750	QNRS	0/0	100.0	100.0	MEG_6020	Drugs:Fluoroquinolones:Quinolone_resistance_protein_Qnr:QNRS	NA
contig00019	11905	12774	ROBA	0/0	100.0	99.1	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00014	65969	66291	SOXS	0/0	99.7	99.7	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00003	344414	345580	UGD	0/0	100.0	95.9	MEG_7328	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:UGD	NA
contig00003	124793	126436	YOGI	0/0	100.0	98.2	MEG_7842	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:YOGI	NA

ID256

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00057	3157	3945	aadA5_1	0/0	100	100.0	AF137361	aadA5	Streptomycin
contig00066	843	1646	aph(3’’)-Ib_5	0/0	100	100.0	AF321551	aph(3’’)-Ib	Streptomycin
contig00066	7	843	aph(6)-Id_1	0/0	100	100.0	M28829	aph(6)-Id	Streptomycin
contig00019	80141	81016	blaCTX-M-15_1	0/0	100	100.0	AY044436	blaCTX-M-15	Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig00081	534	1394	blaTEM-1B_1	0/0	100	100.0	AY458016	blaTEM-1B	Amoxicillin, Ampicillin, Cephalothin, Piperacillin, Ticarcillin
contig00057	4076	4549	dfrA17_1	0/0	100	100.0	FJ460238	dfrA17	Trimethoprim
contig00001	64075	65307	mdf(A)_1	0/0	100	97.8	Y08743	mdf(A)
contig00087	69	990	mph(A)_2	1/1	100	99.7	U36578	mph(A)	Erythromycin, Azithromycin, Spiramycin, Telithromycin
contig00057	1771	2637	sul1_5	0/0	100	99.9	EU780013	sul1	Sulfamethoxazole
contig00066	1707	2522	sul2_3	0/0	100	100.0	HQ840942	sul2	Sulfamethoxazole

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00057	3157	3945	aadA5	0/0	100.0	100.0	AF137361:63-852	aadA5 is an aminoglycoside nucleotidyltransferase gene encoded by plasmids transposons and integrons in E. coli K. pneumoniae Kluyvera georgiana P. aeruginosa and E. cloacae	aminoglycoside
contig00001	445341	448490	acrB	0/0	100.0	98.8	U00096.3:484403-481253	Protein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug/proton antiporter.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00006	118145	121258	acrD	0/0	100.0	98.6	AP009048.1:2586250-2589364	AcrD is an aminoglycoside efflux pump expressed in E. coli. Its expression can be induced by indole and is regulated by baeRS and cpxAR.	aminoglycoside
contig00003	345872	347029	acrE	0/0	100.0	98.8	U00096:3413863-3415021	AcrE is a membrane fusion protein similar to AcrA.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00003	347041	350145	acrF	0/0	100.0	96.6	U00096:3415032-3418137	AcrF is a inner membrane transporter similar to AcrB.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00003	344811	345473	acrS	0/0	100.0	98.3	U00096:3413465-3412802	AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.	cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00066	843	1646	APH(3’’)-Ib	0/0	100.0	99.8	AF313472:15593-16397	APH(3’’)-Ib is an aminoglycoside phosphotransferase encoded by plasmids transposons integrative conjugative elements and chromosomes in Enterobacteriaceae and Pseudomonas spp.	aminoglycoside
contig00066	7	843	APH(6)-Id	0/0	100.0	99.9	AF024602:3155-3992	APH(6)-Id is an aminoglycoside phosphotransferase encoded by plasmids integrative conjugative elements and chromosomal genomic islands in K. pneumoniae Salmonella spp. E. coli Shigella flexneri Providencia alcalifaciens Pseudomonas spp. V. cholerae Edwardsiella tarda Pasteurella multocida and Aeromonas bestiarum	aminoglycoside
contig00003	143341	144160	bacA	0/0	99.8	98.3	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00002	83650	84371	baeR	0/0	99.9	97.1	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00002	82250	83653	baeS	0/0	100.0	90.6	AP009048:2165012-2166416	BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.	aminocoumarin, aminoglycoside
contig00009	99254	100627	cpxA	0/0	100.0	98.5	BA000007.3:4905062-4903688	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	aminocoumarin, aminoglycoside
contig00030	15089	15721	CRP	0/0	100.0	99.2	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00019	80141	81016	CTX-M-15	0/0	100.0	100.0	AY044436:1435-2311	CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family	cephalosporin
contig00057	4076	4549	dfrA17	0/0	100.0	100.0	DQ838665:0-474	dfrA17 is an integron-encoded dihydrofolate reductase found in Escherichia coli	diaminopyrimidine
contig00028	47795	48967	emrA	0/0	100.0	98.0	AP009048:2810082-2811255	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	fluoroquinolone
contig00028	48984	50522	emrB	0/0	100.0	98.4	U00096:2812615-2814154	emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin.	fluoroquinolone
contig00006	24375	25430	emrK	0/0	100.0	97.7	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00028	47138	47668	emrR	0/0	100.0	98.5	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00006	22837	24375	emrY	0/0	100.0	97.7	D78168:1591-3130	emrY is a multidrug transport that moves substrates across the inner membrane of the Gram-negative E. coli. It is a homolog of emrB.	tetracycline
contig00008	79457	81100	eptA	0/0	100.0	91.3	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00001	444125	445318	Escherichia_coli_acrA	0/0	100.0	99.1	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00008	136942	138075	Escherichia_coli_ampC	0/0	100.0	97.8	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00001	533227	534384	Escherichia_coli_ampH	0/0	100.0	97.1	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig00005	24245	24577	Escherichia_coli_emrE	0/0	100.0	92.2	Z11877.1:485-818	Member of the small MDR (multidrug resistance) family of transporters, in Escherichia coli this protein provides resistance against a number of positively charged compounds including ethidium bromide and erythromycin, proton-dependent secondary transporter which exchanges protons for compound translocation	macrolide
contig00026	16441	16773	Escherichia_coli_emrE	0/0	100.0	98.8	Z11877.1:485-818	Member of the small MDR (multidrug resistance) family of transporters, in Escherichia coli this protein provides resistance against a number of positively charged compounds including ethidium bromide and erythromycin, proton-dependent secondary transporter which exchanges protons for compound translocation	macrolide
contig00001	64075	65307	Escherichia_coli_mdfA	0/0	100.0	96.3	JQ394987:0-1233	Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter.	benzalkonium_chloride, rhodamine, tetracycline
contig00006	25954	26568	evgA	0/0	100.0	99.0	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00006	26573	30166	evgS	0/0	100.0	96.3	U00096:2484373-2487967	EvgS is a sensor protein that phosphorylates the regulatory protein EvgA. evgS corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	fluoroquinolone, macrolide, penam, tetracycline
contig00004	130808	131536	gadW	0/0	100.0	99.9	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig00004	131905	132729	gadX	0/0	100.0	93.7	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00007	129422	129835	H-NS	0/0	100.0	99.3	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00001	219428	220100	kdpE	0/0	99.3	95.5	U00096.3:721733-721055	kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding.	aminoglycoside
contig00018	28549	28932	marA	0/0	100.0	99.0	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00002	73390	74637	mdtA	0/0	100.0	95.8	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00002	74637	77759	mdtB	0/0	100.0	96.1	U00096:2155262-2158385	MdtB is a transporter that forms a heteromultimer complex with MdtC to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex.	aminocoumarin
contig00002	77760	80837	mdtC	0/0	100.0	94.0	U00096:2158385-2161463	MdtC is a transporter that forms a heteromultimer complex with MdtB to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex. In the absence of MdtB MdtC can form a homomultimer complex that results in a functioning efflux complex with a narrower drug specificity. mdtC corresponds to 3 loci in Pseudomonas aeruginosa PAO1 (gene name: muxC/muxB) and 3 loci in Pseudomonas aeruginosa LESB58.	aminocoumarin
contig00004	126150	127307	mdtE	0/0	100.0	98.3	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00004	127332	130445	mdtF	0/0	100.0	97.1	U00096:3660413-3663527	MdtF is the multidrug inner membrane transporter for the MdtEF-TolC efflux complex.	fluoroquinolone, macrolide, penam
contig00017	93527	94753	mdtG	0/0	100.0	98.4	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00017	83689	84897	mdtH	0/0	100.0	98.3	U00096:1125326-1124117	Multidrug resistance protein MdtH	fluoroquinolone
contig00046	261	1472	mdtM	0/0	98.3	95.5	U00096.3:4568519-4567286	Multidrug resistance protein MdtM	acridine_dye, fluoroquinolone, lincosamide, nucleoside, phenicol
contig00008	49203	50234	mdtN	0/0	100.0	96.3	AP009048.1:4307588-4306556	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	acridine_dye, nucleoside
contig00008	47152	49203	mdtO	0/0	100.0	97.2	AP009048.1:4306557-4304505	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00008	45689	47155	mdtP	0/0	100.0	98.1	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00087	69	974	mphA	0/0	100.0	100.0	D16251.1:2531-1625	The mphA gene encodes for resistance enzyme MPH(2’)-I which preferentially inactivate 14-membered macrolides (e.g.erythromycin telithromycin roxithromycin) over 16-membered macrolides (e.g.tylosin spiramycin). It phosphorylates macrolides at 2’-OH hydroxyl of desosamine sugar of macrolides in a GTP-dependent manner.	macrolide
contig00010	48842	50590	msbA	0/0	100.0	98.1	U00096.3:966620-968369	MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability.	nitroimidazole
contig00002	283849	284817	pmrF	0/0	100.0	97.6	U00096:2367070-2368039	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide
contig00057	1771	2610	sul1	0/0	100.0	100.0	JF969163:1053-1893	Sul1 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria. It is linked to other resistance genes of class 1 integrons.	sulfonamide
contig00066	1707	2522	sul2	0/0	100.0	99.6	AY055428.1:21084-20268	Sul2 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria usually found on small plasmids.	sulfonamide
contig00081	534	1394	TEM-1	0/0	100.0	99.9	AL513383:161910-162771	TEM-1 is a broad-spectrum beta-lactamase found in many Gram-negative bacteria. Confers resistance to penicillins and first generation cephalosphorins.	cephalosporin, monobactam, penam, penem
contig00003	116171	117658	tolC	0/0	100.0	98.2	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan
contig00002	18552	19718	ugd	0/0	100.0	99.9	U00096:2099613-2098446	PmrE is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin	peptide
contig00002	223977	225620	yojI	0/0	100.0	97.3	U00096.3:2308615-2306971	YojI mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. YojI is capable of pumping out microcin molecules. The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI.	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00057	3157	3945	(AGly)aadA5	0/0	100	100.0	AF137361:64-852	(AGly)aadA5	NA
contig00066	843	1646	(AGly)strA	0/0	100	99.9	AB366441:22458-23261	(AGly)strA	NA
contig00066	7	843	(AGly)strB	0/0	100	100.0	FJ474091:264-1100	(AGly)strB	NA
contig00008	136942	138075	(Bla)AmpC2_Ecoli	0/0	100	97.8	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00001	533227	534384	(Bla)ampH_Ecoli	0/0	100	97.1	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00019	80141	81016	(Bla)blaCTX-M-15	0/0	100	100.0	JQ686199:261-1136	(Bla)blaCTX-M-15	NA
contig00081	534	1394	(Bla)blaTEM-105	0/0	100	99.9	AF516720:215-1075	(Bla)blaTEM-105	NA
contig00001	278645	280546	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100	98.7	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA
contig00087	69	974	(MLS)mph(A)	0/0	100	100.0	DQ445270:1626-2531	(MLS)mph(A)	NA
contig00057	1771	2610	(Sul)sul1	0/0	100	100.0	AF071413:6700-7539	(Sul)sul1	NA
contig00066	1707	2522	(Sul)sul2	0/0	100	99.6	EU360945:1617-2432	(Sul)sul2	NA
contig00057	4076	4549	(Tmt)dfrA17	0/0	100	100.0	AB126604:98-571	(Tmt)dfrA17	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00057	3157	3945	aadA5	0/0	100	100.0	NG_047357.1	ANT(3’’)-Ia family aminoglycoside nucleotidyltransferase AadA5	STREPTOMYCIN
contig00066	843	1670	aph(3’’)-Ib	0/0	100	100.0	NG_056002.2	aminoglycoside O-phosphotransferase APH(3’’)-Ib	STREPTOMYCIN
contig00066	7	843	aph(6)-Id	0/0	100	100.0	NG_047464.1	aminoglycoside O-phosphotransferase APH(6)-Id	STREPTOMYCIN
contig00019	80141	81016	blaCTX-M-15	0/0	100	100.0	NG_048935.1	class A extended-spectrum beta-lactamase CTX-M-15	CEPHALOSPORIN
contig00008	136942	138075	blaEC-5	0/0	100	99.5	NG_049085.1	cephalosporin-hydrolyzing class C beta-lactamase EC-5	CEPHALOSPORIN
contig00081	534	1394	blaTEM-1	0/0	100	100.0	NG_050145.1	class A broad-spectrum beta-lactamase TEM-1	BETA-LACTAM
contig00057	4076	4549	dfrA17	0/0	100	99.8	NG_047710.1	trimethoprim-resistant dihydrofolate reductase DfrA17	TRIMETHOPRIM
contig00087	69	990	mph(A)	1/1	100	99.7	NG_047986.1	Mph(A) family macrolide 2’-phosphotransferase	MACROLIDE
contig00057	1771	2610	sul1	0/0	100	100.0	NG_048082.1	sulfonamide-resistant dihydropteroate synthase Sul1	SULFONAMIDE
contig00066	1707	2522	sul2	0/0	100	99.9	NG_048118.1	sulfonamide-resistant dihydropteroate synthase Sul2	SULFONAMIDE

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00001	444125	445318	ACRA	0/0	100.0	99.1	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00001	445341	448490	ACRB	0/0	100.0	98.8	MEG_401	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRB	NA
contig00006	118145	121258	ACRD	0/0	100.0	98.6	MEG_407	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ACRD	NA
contig00003	345872	347029	ACRE	0/0	100.0	98.8	MEG_408	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRE	NA
contig00003	347041	350145	ACRF	0/0	100.0	96.6	MEG_409	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRF	NA
contig00003	344811	345473	ACRS	0/0	100.0	98.3	MEG_415	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS	NA
contig00001	533227	534384	AMPH	0/0	100.0	97.1	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00057	3157	3945	ANT3-DPRIME	0/0	100.0	100.0	MEG_928	Drugs:Aminoglycosides:Aminoglycoside_O-nucleotidyltransferases:ANT3-DPRIME	NA
contig00066	843	1670	APH3-DPRIME	0/0	100.0	100.0	MEG_1019	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH3-DPRIME	NA
contig00066	7	843	APH6	0/0	100.0	100.0	MEG_1086	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH6	NA
contig00002	59211	61063	ASMA	0/0	100.0	97.8	MEG_1180	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:ASMA	NA
contig00003	143341	144160	BACA	0/0	99.8	98.5	MEG_1189	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00002	83650	84371	BAER	0/0	99.9	97.1	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00002	82250	83653	BAES	0/0	100.0	90.6	MEG_1193	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES	NA
contig00002	199154	200344	BCR	0/0	100.0	96.6	MEG_1210	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR	NA
contig00008	136942	138075	BLAEC	0/0	100.0	99.5	MEG_1275	Drugs:betalactams:Class_C_betalactamases:BLAEC	NA
contig00009	98559	99257	CPXAR	0/0	100.0	97.8	MEG_2118	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00009	99254	100627	CPXAR	0/0	100.0	98.9	MEG_2121	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00030	15089	15721	CRP	0/0	100.0	99.2	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00057	4076	4549	DFRA	0/0	100.0	100.0	MEG_2547	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00028	47795	48967	EMRA	0/0	100.0	98.0	MEG_2722	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA	NA
contig00028	48984	50522	EMRB	0/0	100.0	98.4	MEG_2725	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRB	NA
contig00016	21518	22708	EMRD	0/0	100.0	97.6	MEG_2729	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD	NA
contig00006	24375	25538	EMRK	0/0	100.0	97.4	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig00028	47138	47668	EMRR	0/0	100.0	98.5	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00006	22837	24375	EMRY	0/0	100.0	97.7	MEG_2736	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRY	NA
contig00008	79457	81100	EPTA	0/0	100.0	91.3	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig00006	26573	30166	EVGS	0/0	100.0	97.4	MEG_2869	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EVGS	NA
contig00004	130808	131536	GADW	0/0	100.0	99.9	MEG_3082	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig00004	131905	132729	GADX	0/0	100.0	93.7	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00007	129422	129835	HNS	0/0	100.0	99.3	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00001	219428	220100	KDPE	0/0	99.3	95.5	MEG_3448	Drugs:Aminoglycosides:Aminoglycoside_efflux_pumps:KDPE	NA
contig00018	28543	28932	MARA	0/0	100.0	99.0	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00018	28094	28528	MARR	0/0	100.0	97.9	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00001	64075	65307	MDFA	0/0	100.0	97.9	MEG_3737	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDFA	NA
contig00002	73390	74637	MDTA	0/0	100.0	95.8	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00002	74637	77759	MDTB	0/0	100.0	96.1	MEG_3747	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTB	NA
contig00002	77760	80837	MDTC	0/0	100.0	94.0	MEG_3749	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTC	NA
contig00004	126150	127307	MDTE	0/0	100.0	98.3	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00004	127332	130445	MDTF	0/0	100.0	97.1	MEG_3752	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTF	NA
contig00017	93527	94753	MDTG	0/0	100.0	98.5	MEG_3753	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig00017	83689	84897	MDTH	0/0	100.0	98.3	MEG_3755	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTH	NA
contig00018	59497	59826	MDTI	0/0	100.0	98.8	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00018	59813	60178	MDTJ	0/0	100.0	98.4	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00005	282364	283736	MDTK	0/0	99.9	97.7	MEG_3759	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:MDTK	NA
contig00046	261	1472	MDTM	0/0	98.3	95.5	MEG_3761	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTM	NA
contig00008	49203	50234	MDTN	0/0	100.0	96.3	MEG_3763	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN	NA
contig00008	47152	49203	MDTO	0/0	100.0	97.2	MEG_3764	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTO	NA
contig00008	45689	47155	MDTP	0/0	100.0	98.1	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig00087	69	990	MPHA	1/1	100.0	99.7	MEG_4030	Drugs:MLS:Macrolide_phosphotransferases:MPHA	NA
contig00010	48842	50590	MSBA	0/0	100.0	98.1	MEG_4061	Drugs:Multi-drug_resistance:Multi-drug_ABC_efflux_pumps:MSBA	NA
contig00005	24245	24577	MVRC	0/0	100.0	92.2	MEG_4103	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MVRC	NA
contig00026	16441	16773	MVRC	0/0	100.0	98.8	MEG_4103	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MVRC	NA
contig00001	278645	280546	PBP2	0/0	100.0	98.7	MEG_5400	Drugs:betalactams:Penicillin_binding_protein:PBP2	NA
contig00002	283849	284817	PMRF	0/0	100.0	97.6	MEG_5801	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF	NA
contig00014	47049	47918	ROBA	0/0	100.0	99.7	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00008	17336	17658	SOXS	0/0	99.7	98.1	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00057	1644	2611	SULI	0/0	100.0	100.0	MEG_6615	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULI	NA
contig00066	1707	2522	SULII	0/0	100.0	100.0	MEG_6618	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULII	NA
contig00081	516	1761	TEM	0/0	98.3	99.4	MEG_6875	Drugs:betalactams:Class_A_betalactamases:TEM	NA
contig00002	18552	19718	UGD	0/0	100.0	99.9	MEG_7328	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:UGD	NA
contig00002	223977	225620	YOGI	0/0	100.0	97.3	MEG_7842	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:YOGI	NA

ID263

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00074	4779	5639	aac(3)-IId_1	0/0	100.0	99.9	EU022314	aac(3)-IId	Gentamicin, Tobramycin
contig00061	8986	9787	aadA2_1	0/0	97.9	99.9	NC_010870	aadA2	Streptomycin
contig00058	14043	14846	aph(3’’)-Ib_5	0/0	100.0	100.0	AF321551	aph(3’’)-Ib	Streptomycin
contig00058	13207	14043	aph(6)-Id_1	0/0	100.0	99.9	M28829	aph(6)-Id	Streptomycin
contig00066	2636	3511	blaCTX-M-15_1	0/0	100.0	100.0	AY044436	blaCTX-M-15	Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig00061	1421	2080	catA1_1	0/0	100.0	99.8	V00622	catA1	Chloramphenicol
contig00061	8091	8588	dfrA12_8	0/0	100.0	100.0	AM040708	dfrA12	Trimethoprim
contig00099	42	551	dfrA8_1	0/0	100.0	100.0	U10186	dfrA8	Trimethoprim
contig00004	7373	8605	mdf(A)_1	0/0	100.0	99.9	Y08743	mdf(A)
contig00058	7749	8670	mph(A)_2	1/1	100.0	99.6	U36578	mph(A)	Erythromycin, Azithromycin, Spiramycin, Telithromycin
contig00061	10265	11131	sul1_5	0/0	100.0	99.9	EU780013	sul1	Sulfamethoxazole
contig00058	14907	15722	sul2_2	0/0	100.0	100.0	AY034138	sul2	Sulfamethoxazole
contig00082	813	2018	tet(B)_2	0/0	100.0	100.0	AF326777	tet(B)	Doxycycline, Tetracycline, Minocycline

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00074	4779	5639	AAC(3)-IId	0/0	100.0	99.9	EU022314.1:0-861	AAC(3)-IId is a plasmid-encoded aminoglycoside acetyltransferase in E. coli	aminoglycoside
contig00061	9008	9787	aadA2	0/0	100.0	99.9	AF156486:5012-5792	aadA2 is an aminoglycoside nucleotidyltransferase gene encoded by plasmids and integrons in K. pneumoniae Salmonella spp. Corynebacterium glutamicum C. freundii and Aeromonas spp.	aminoglycoside
contig00005	41369	44518	acrB	0/0	100.0	100.0	U00096.3:484403-481253	Protein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug/proton antiporter.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00003	135681	138794	acrD	0/0	100.0	100.0	AP009048.1:2586250-2589364	AcrD is an aminoglycoside efflux pump expressed in E. coli. Its expression can be induced by indole and is regulated by baeRS and cpxAR.	aminoglycoside
contig00031	8641	9798	acrE	0/0	100.0	99.9	U00096:3413863-3415021	AcrE is a membrane fusion protein similar to AcrA.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00031	5525	8629	acrF	0/0	100.0	99.9	U00096:3415032-3418137	AcrF is a inner membrane transporter similar to AcrB.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00031	10197	10859	acrS	0/0	100.0	100.0	U00096:3413465-3412802	AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.	cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00058	14043	14846	APH(3’’)-Ib	0/0	100.0	99.8	AF313472:15593-16397	APH(3’’)-Ib is an aminoglycoside phosphotransferase encoded by plasmids transposons integrative conjugative elements and chromosomes in Enterobacteriaceae and Pseudomonas spp.	aminoglycoside
contig00058	13207	14043	APH(6)-Id	0/0	100.0	99.8	AF024602:3155-3992	APH(6)-Id is an aminoglycoside phosphotransferase encoded by plasmids integrative conjugative elements and chromosomal genomic islands in K. pneumoniae Salmonella spp. E. coli Shigella flexneri Providencia alcalifaciens Pseudomonas spp. V. cholerae Edwardsiella tarda Pasteurella multocida and Aeromonas bestiarum	aminoglycoside
contig00014	115946	116767	bacA	0/0	100.0	98.7	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00041	10771	11493	baeR	0/0	100.0	100.0	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00041	9371	10774	baeS	0/0	100.0	99.9	AP009048:2165012-2166416	BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.	aminocoumarin, aminoglycoside
contig00061	1421	2080	catI	0/0	100.0	99.8	V00622:243-903	catI is a chromosome and transposon-encoded variant of the cat gene found in Escherichia coli and Acinetobacter baumannii	phenicol
contig00012	61493	62866	cpxA	0/0	100.0	99.0	BA000007.3:4905062-4903688	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	aminocoumarin, aminoglycoside
contig00007	15377	16009	CRP	0/0	100.0	99.4	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00066	2636	3511	CTX-M-15	0/0	100.0	100.0	AY044436:1435-2311	CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family	cephalosporin
contig00061	8091	8588	dfrA12	0/0	100.0	100.0	GU585907.1:22103-21605	dfrA12 is an integron-encoded dihydrofolate reductase found in Vibrio cholerae	diaminopyrimidine
contig00099	42	551	dfrA8	0/0	100.0	100.0	KJ174469:710-1220	dfrA8 is a transposon-encoded dihydrofolate reductase found in Salmonella enterica	diaminopyrimidine
contig00006	58060	59232	emrA	0/0	100.0	100.0	AP009048:2810082-2811255	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	fluoroquinolone
contig00006	59249	60787	emrB	0/0	100.0	100.0	U00096:2812615-2814154	emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin.	fluoroquinolone
contig00009	121400	122455	emrK	0/0	100.0	99.9	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00006	57403	57933	emrR	0/0	100.0	99.8	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00009	119862	121400	emrY	0/0	100.0	99.9	D78168:1591-3130	emrY is a multidrug transport that moves substrates across the inner membrane of the Gram-negative E. coli. It is a homolog of emrB.	tetracycline
contig00042	18804	20447	eptA	0/0	100.0	99.9	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00005	40153	41346	Escherichia_coli_acrA	0/0	100.0	100.0	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00025	65396	66529	Escherichia_coli_ampC	0/0	100.0	97.3	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00003	170193	171497	Escherichia_coli_ampC1_beta-lactamase	0/0	100.0	99.9	FN649414.1:2765050-2766355	An ampC-like beta-lactamase identified from Escherichia coli.	cephalosporin, penam
contig00005	129381	130538	Escherichia_coli_ampH	0/0	100.0	100.0	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig00004	7373	8605	Escherichia_coli_mdfA	0/0	100.0	98.4	JQ394987:0-1233	Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter.	benzalkonium_chloride, rhodamine, tetracycline
contig00009	122978	123592	evgA	0/0	100.0	100.0	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00009	123597	127190	evgS	0/0	100.0	100.0	U00096:2484373-2487967	EvgS is a sensor protein that phosphorylates the regulatory protein EvgA. evgS corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	fluoroquinolone, macrolide, penam, tetracycline
contig00038	2242	2970	gadW	0/0	100.0	94.7	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig00038	1051	1875	gadX	0/0	100.0	100.0	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00026	62969	63382	H-NS	0/0	100.0	99.3	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00013	8325	9002	kdpE	0/0	100.0	100.0	U00096.3:721733-721055	kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding.	aminoglycoside
contig00001	231027	231410	marA	0/0	100.0	100.0	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00041	511	1758	mdtA	0/0	100.0	98.0	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00041	1758	4880	mdtB	0/0	100.0	97.0	U00096:2155262-2158385	MdtB is a transporter that forms a heteromultimer complex with MdtC to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex.	aminocoumarin
contig00041	4881	7958	mdtC	0/0	100.0	98.0	U00096:2158385-2161463	MdtC is a transporter that forms a heteromultimer complex with MdtB to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex. In the absence of MdtB MdtC can form a homomultimer complex that results in a functioning efflux complex with a narrower drug specificity. mdtC corresponds to 3 loci in Pseudomonas aeruginosa PAO1 (gene name: muxC/muxB) and 3 loci in Pseudomonas aeruginosa LESB58.	aminocoumarin
contig00038	6471	7628	mdtE	0/0	100.0	100.0	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00038	3333	6446	mdtF	0/0	100.0	100.0	U00096:3660413-3663527	MdtF is the multidrug inner membrane transporter for the MdtEF-TolC efflux complex.	fluoroquinolone, macrolide, penam
contig00017	16615	17841	mdtG	0/0	100.0	99.4	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00017	26470	27678	mdtH	0/0	100.0	99.9	U00096:1125326-1124117	Multidrug resistance protein MdtH	fluoroquinolone
contig00047	473	1684	mdtM	0/0	98.3	95.5	U00096.3:4568519-4567286	Multidrug resistance protein MdtM	acridine_dye, fluoroquinolone, lincosamide, nucleoside, phenicol
contig00034	10883	11914	mdtN	0/0	100.0	100.0	AP009048.1:4307588-4306556	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	acridine_dye, nucleoside
contig00034	11914	13965	mdtO	0/0	100.0	100.0	AP009048.1:4306557-4304505	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00034	13962	15428	mdtP	0/0	100.0	100.0	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00058	7749	8654	mphA	0/0	100.0	99.9	D16251.1:2531-1625	The mphA gene encodes for resistance enzyme MPH(2’)-I which preferentially inactivate 14-membered macrolides (e.g.erythromycin telithromycin roxithromycin) over 16-membered macrolides (e.g.tylosin spiramycin). It phosphorylates macrolides at 2’-OH hydroxyl of desosamine sugar of macrolides in a GTP-dependent manner.	macrolide
contig00003	114519	114995	mphB	0/0	100.0	98.3	AE005174.2:3397370-3397847	The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides.	macrolide
contig00004	90321	92069	msbA	0/0	100.0	100.0	U00096.3:966620-968369	MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability.	nitroimidazole
contig00009	17667	18635	pmrF	0/0	100.0	100.0	U00096:2367070-2368039	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide
contig00061	10292	11131	sul1	0/0	100.0	100.0	JF969163:1053-1893	Sul1 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria. It is linked to other resistance genes of class 1 integrons.	sulfonamide
contig00058	14907	15722	sul2	0/0	100.0	100.0	AY055428.1:21084-20268	Sul2 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria usually found on small plasmids.	sulfonamide
contig00082	813	2018	tet(B)	0/0	100.0	99.8	AB089595:0-1206	Tet(B) is a tetracycline efflux protein expressed in many Gram-negative bacteria. It confers resistance to tetracycline doxycycline and minocycline but not tigecycline.	tetracycline
contig00014	92082	93569	tolC	0/0	100.0	99.7	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan
contig00036	42513	44156	yojI	0/0	100.0	100.0	U00096.3:2308615-2306971	YojI mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. YojI is capable of pumping out microcin molecules. The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI.	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00074	4779	5639	(AGly)aac3-IId	0/0	100	99.9	EU022314:1-861	(AGly)aac3-IId	NA
contig00061	9008	9787	(AGly)aadA2	0/0	100	99.9	X68227:66-945	(AGly)aadA2	NA
contig00058	14043	14846	(AGly)strA	0/0	100	99.9	AB366441:22458-23261	(AGly)strA	NA
contig00058	13207	14043	(AGly)strB	0/0	100	99.9	FJ474091:264-1100	(AGly)strB	NA
contig00003	170193	171497	(Bla)AmpC1_Ecoli	0/0	100	99.9	FN649414:2765051-2766355	(Bla)AmpC1_Ecoli	NA
contig00025	65396	66529	(Bla)AmpC2_Ecoli	0/0	100	97.3	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00005	129381	130538	(Bla)ampH_Ecoli	0/0	100	100.0	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00066	2636	3511	(Bla)blaCTX-M-15	0/0	100	100.0	JQ686199:261-1136	(Bla)blaCTX-M-15	NA
contig00013	60412	62313	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100	100.0	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA
contig00058	7749	8654	(MLS)mph(A)	0/0	100	99.9	DQ445270:1626-2531	(MLS)mph(A)	NA
contig00061	1421	2080	(Phe)catA1	0/0	100	99.8	V00622:244-903	(Phe)catA1	NA
contig00061	10292	11131	(Sul)sul1	0/0	100	100.0	AF071413:6700-7539	(Sul)sul1	NA
contig00058	14907	15722	(Sul)sul2	0/0	100	100.0	EU360945:1617-2432	(Sul)sul2	NA
contig00082	813	2018	(Tet)tetB	0/0	100	99.7	AB089594:1-1206	(Tet)tetB	NA
contig00061	8091	8588	(Tmt)dfrA12	0/0	100	100.0	Z21672:310-807	(Tmt)dfrA12	NA
contig00099	42	551	(Tmt)dfrA8	0/0	100	100.0	U10186:711-1220	(Tmt)dfrA8	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00074	4779	5639	aac(3)-IId	0/0	100	100.0	NG_047251.1	aminoglycoside N-acetyltransferase AAC(3)-IId	GENTAMICIN
contig00061	8996	9787	aadA2	0/0	100	100.0	NG_047343.1	ANT(3’’)-Ia family aminoglycoside nucleotidyltransferase AadA2	STREPTOMYCIN
contig00058	14043	14870	aph(3’’)-Ib	0/0	100	100.0	NG_056002.2	aminoglycoside O-phosphotransferase APH(3’’)-Ib	STREPTOMYCIN
contig00058	13207	14043	aph(6)-Id	0/0	100	100.0	NG_047466.1	aminoglycoside O-phosphotransferase APH(6)-Id	STREPTOMYCIN
contig00066	2636	3511	blaCTX-M-15	0/0	100	100.0	NG_048935.1	class A extended-spectrum beta-lactamase CTX-M-15	CEPHALOSPORIN
contig00025	65396	66529	blaEC-15	0/0	100	98.5	NG_049081.1	class C extended-spectrum beta-lactamase EC-15	CEPHALOSPORIN
contig00061	1421	2080	catA1	0/0	100	99.8	NG_047582.1	type A-1 chloramphenicol O-acetyltransferase	CHLORAMPHENICOL
contig00061	8091	8588	dfrA12	0/0	100	100.0	NG_047689.1	trimethoprim-resistant dihydrofolate reductase DfrA12	TRIMETHOPRIM
contig00099	42	551	dfrA8	0/0	100	100.0	NG_047741.1	trimethoprim-resistant dihydrofolate reductase DfrA8	TRIMETHOPRIM
contig00058	7749	8670	mph(A)	1/1	100	99.6	NG_047986.1	Mph(A) family macrolide 2’-phosphotransferase	MACROLIDE
contig00061	10292	11131	sul1	0/0	100	100.0	NG_048082.1	sulfonamide-resistant dihydropteroate synthase Sul1	SULFONAMIDE
contig00058	14907	15722	sul2	0/0	100	100.0	NG_051852.1	sulfonamide-resistant dihydropteroate synthase Sul2	SULFONAMIDE
contig00082	813	2018	tet(B)	0/0	100	100.0	NG_048163.1	tetracycline efflux MFS transporter Tet(B)	TETRACYCLINE

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00074	4779	5639	AAC3	0/0	100.0	100.0	MEG_64	Drugs:Aminoglycosides:Aminoglycoside_N-acetyltransferases:AAC3	NA
contig00005	40153	41346	ACRA	0/0	100.0	100.0	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00005	41369	44518	ACRB	0/0	100.0	100.0	MEG_401	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRB	NA
contig00003	135681	138794	ACRD	0/0	100.0	100.0	MEG_407	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ACRD	NA
contig00031	8641	9798	ACRE	0/0	100.0	99.9	MEG_408	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRE	NA
contig00031	5525	8629	ACRF	0/0	100.0	99.9	MEG_409	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRF	NA
contig00031	10197	10859	ACRS	0/0	100.0	100.0	MEG_415	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS	NA
contig00005	129381	130538	AMPH	0/0	100.0	100.0	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00061	8986	9787	ANT3-DPRIME	0/0	97.9	99.9	MEG_975	Drugs:Aminoglycosides:Aminoglycoside_O-nucleotidyltransferases:ANT3-DPRIME	NA
contig00058	14043	14870	APH3-DPRIME	0/0	100.0	100.0	MEG_1019	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH3-DPRIME	NA
contig00058	13207	14043	APH6	0/0	100.0	100.0	MEG_1084	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH6	NA
contig00027	52233	54085	ASMA	0/0	100.0	97.0	MEG_1180	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:ASMA	NA
contig00014	115946	116767	BACA	0/0	100.0	98.9	MEG_1189	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00041	10771	11493	BAER	0/0	100.0	100.0	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00041	9371	10774	BAES	0/0	100.0	99.9	MEG_1193	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES	NA
contig00019	67605	68795	BCR	0/0	100.0	99.9	MEG_1210	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR	NA
contig00025	65396	66529	BLAEC	0/0	100.0	98.5	MEG_1282	Drugs:betalactams:Class_C_betalactamases:BLAEC	NA
contig00061	1416	2080	CATA	0/0	99.1	100.0	MEG_1593	Drugs:Phenicol:Chloramphenicol_acetyltransferases:CATA	NA
contig00012	60798	61496	CPXAR	0/0	100.0	100.0	MEG_2122	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00012	61493	62866	CPXAR	0/0	100.0	100.0	MEG_2121	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00007	15377	16009	CRP	0/0	100.0	99.4	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00070	3603	4545	CTX	0/0	100.0	98.2	MEG_2435	Drugs:betalactams:Class_A_betalactamases:CTX	NA
contig00061	8091	8588	DFRA	0/0	100.0	100.0	MEG_2551	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00099	42	551	DFRA	0/0	100.0	100.0	MEG_2553	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00006	58060	59232	EMRA	0/0	100.0	100.0	MEG_2722	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA	NA
contig00006	59249	60787	EMRB	0/0	100.0	100.0	MEG_2725	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRB	NA
contig00011	36205	37395	EMRD	0/0	100.0	100.0	MEG_2729	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD	NA
contig00009	121400	122563	EMRK	0/0	100.0	99.9	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig00006	57403	57933	EMRR	0/0	100.0	99.8	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00009	119862	121400	EMRY	0/0	100.0	99.9	MEG_2736	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRY	NA
contig00042	18804	20447	EPTA	0/0	100.0	99.9	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig00009	123597	127190	EVGS	0/0	100.0	100.0	MEG_2870	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EVGS	NA
contig00038	2242	2970	GADW	0/0	100.0	100.0	MEG_3081	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig00038	1051	1875	GADX	0/0	100.0	100.0	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00026	62969	63382	HNS	0/0	100.0	99.3	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00013	8325	9002	KDPE	0/0	100.0	100.0	MEG_3448	Drugs:Aminoglycosides:Aminoglycoside_efflux_pumps:KDPE	NA
contig00001	231027	231416	MARA	0/0	100.0	100.0	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00001	231430	231864	MARR	0/0	100.0	100.0	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00004	7373	8605	MDFA	0/0	100.0	100.0	MEG_3737	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDFA	NA
contig00041	511	1758	MDTA	0/0	100.0	98.0	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00041	1758	4880	MDTB	0/0	100.0	97.0	MEG_3747	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTB	NA
contig00041	4881	7958	MDTC	0/0	100.0	98.0	MEG_3749	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTC	NA
contig00038	6471	7628	MDTE	0/0	100.0	100.0	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00038	3333	6446	MDTF	0/0	100.0	100.0	MEG_3752	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTF	NA
contig00017	16615	17841	MDTG	0/0	100.0	100.0	MEG_3753	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig00017	26470	27678	MDTH	0/0	100.0	99.9	MEG_3755	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTH	NA
contig00001	198306	198635	MDTI	0/0	100.0	100.0	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00001	197954	198319	MDTJ	0/0	100.0	99.5	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00001	126552	127925	MDTK	0/0	100.0	100.0	MEG_3759	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:MDTK	NA
contig00047	473	1684	MDTM	0/0	98.3	95.5	MEG_3761	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTM	NA
contig00034	10883	11914	MDTN	0/0	100.0	100.0	MEG_3763	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN	NA
contig00034	11914	13965	MDTO	0/0	100.0	100.0	MEG_3764	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTO	NA
contig00034	13962	15428	MDTP	0/0	100.0	100.0	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig00058	7749	8670	MPHA	1/1	100.0	99.6	MEG_4030	Drugs:MLS:Macrolide_phosphotransferases:MPHA	NA
contig00003	114519	114995	MPHB	0/0	100.0	98.3	MEG_4033	Drugs:MLS:Macrolide_phosphotransferases:MPHB	NA
contig00004	90321	92069	MSBA	0/0	100.0	100.0	MEG_4061	Drugs:Multi-drug_resistance:Multi-drug_ABC_efflux_pumps:MSBA	NA
contig00013	60412	62313	PBP2	0/0	100.0	100.0	MEG_5400	Drugs:betalactams:Penicillin_binding_protein:PBP2	NA
contig00003	170193	171497	PBP4B	0/0	100.0	99.9	MEG_5409	Drugs:betalactams:Penicillin_binding_protein:PBP4B	NA
contig00009	17667	18635	PMRF	0/0	100.0	100.0	MEG_5801	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF	NA
contig00037	4214	5083	ROBA	0/0	100.0	99.0	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00034	37045	37368	SOXS	0/0	100.0	100.0	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00061	10291	11258	SULI	0/0	100.0	100.0	MEG_6615	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULI	NA
contig00058	14907	15722	SULII	0/0	100.0	100.0	MEG_6617	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULII	NA
contig00082	813	2018	TETB	0/0	100.0	100.0	MEG_7052	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETB	NA
contig00036	42513	44156	YOGI	0/0	100.0	100.0	MEG_7842	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:YOGI	NA

ID282

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig01776	68	904	aph(6)-Id_1	0/0	100.0	99.9	M28829	aph(6)-Id	Streptomycin
contig00490	119	994	blaCTX-M-15_1	0/0	100.0	100.0	AY044436	blaCTX-M-15	Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig01803	123	953	blaOXA-1_1	0/0	100.0	100.0	HQ170510	blaOXA-1	Amoxicillin, Amoxicillin+Clavulanic_acid, Ampicillin, Ampicillin+Clavulanic_acid, Cefepime, Piperacillin, Piperacillin+Tazobactam
contig00261	80	940	blaTEM-1B_1	0/0	100.0	100.0	AY458016	blaTEM-1B	Amoxicillin, Ampicillin, Cephalothin, Piperacillin, Ticarcillin
contig00482	221	880	catA1_1	0/0	100.0	99.8	V00622	catA1	Chloramphenicol
contig01778	448	921	dfrA1_10	0/0	100.0	99.8	AF203818	dfrA1	Trimethoprim
contig00214	1061	2293	mdf(A)_1	0/0	100.0	97.6	Y08743	mdf(A)
contig00261	5187	6108	mph(A)_2	1/1	100.0	99.5	U36578	mph(A)	Erythromycin, Azithromycin, Spiramycin, Telithromycin
contig00841	1806	2450	qnrB19_1	0/0	100.0	100.0	EU432277	qnrB19	Ciprofloxacin
contig01015	208	864	qnrS1_1	0/0	100.0	100.0	AB187515	qnrS1	Ciprofloxacin
contig02102	12	827	sul2_2	0/0	100.0	100.0	AY034138	sul2	Sulfamethoxazole
contig00167	601	1847	tet(A)_6	0/0	97.8	99.9	AF534183	tet(A)	Doxycycline, Tetracycline
contig00280	1988	3193	tet(B)_2	0/0	100.0	100.0	AF326777	tet(B)	Doxycycline, Tetracycline, Minocycline

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00136	19	1176	acrE	0/0	100.0	98.8	U00096:3413863-3415021	AcrE is a membrane fusion protein similar to AcrA.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00136	1188	4292	acrF	0/0	100.0	98.0	U00096:3415032-3418137	AcrF is a inner membrane transporter similar to AcrB.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00963	1383	2045	acrS	0/0	100.0	97.1	U00096:3413465-3412802	AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.	cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig01390	771	1433	acrS	0/0	100.0	99.1	U00096:3413465-3412802	AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.	cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig01776	68	904	APH(6)-Id	0/0	100.0	99.8	AF024602:3155-3992	APH(6)-Id is an aminoglycoside phosphotransferase encoded by plasmids integrative conjugative elements and chromosomal genomic islands in K. pneumoniae Salmonella spp. E. coli Shigella flexneri Providencia alcalifaciens Pseudomonas spp. V. cholerae Edwardsiella tarda Pasteurella multocida and Aeromonas bestiarum	aminoglycoside
contig00057	6850	7669	bacA	0/0	99.8	97.6	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00707	1993	2814	bacA	0/0	100.0	99.6	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00482	221	880	catI	0/0	100.0	99.8	V00622:243-903	catI is a chromosome and transposon-encoded variant of the cat gene found in Escherichia coli and Acinetobacter baumannii	phenicol
contig01049	330	1703	cpxA	0/0	100.0	97.8	BA000007.3:4905062-4903688	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	aminocoumarin, aminoglycoside
contig00128	1060	1692	CRP	0/0	100.0	99.0	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00490	119	994	CTX-M-15	0/0	100.0	100.0	AY044436:1435-2311	CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family	cephalosporin
contig01778	448	921	dfrA1	0/0	100.0	100.0	KJ541681.1:19526-20000	dfrA1 is an integron-encoded dihydrofolate reductase	diaminopyrimidine
contig00817	947	2485	emrB	0/0	100.0	98.2	U00096:2812615-2814154	emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin.	fluoroquinolone
contig00048	9955	11010	emrK	0/0	100.0	97.0	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00176	199	1254	emrK	0/0	100.0	99.8	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig01534	47	577	emrR	0/0	100.0	99.4	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig01729	37	567	emrR	0/0	100.0	100.0	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00048	8417	9955	emrY	0/0	100.0	97.4	D78168:1591-3130	emrY is a multidrug transport that moves substrates across the inner membrane of the Gram-negative E. coli. It is a homolog of emrB.	tetracycline
contig00176	1254	2792	emrY	0/0	100.0	99.0	D78168:1591-3130	emrY is a multidrug transport that moves substrates across the inner membrane of the Gram-negative E. coli. It is a homolog of emrB.	tetracycline
contig00227	1151	2284	Escherichia_coli_ampC	0/0	100.0	98.0	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig01434	1	1113	Escherichia_coli_ampC	0/0	98.2	97.3	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00296	3369	4673	Escherichia_coli_ampC1_beta-lactamase	0/0	100.0	99.2	FN649414.1:2765050-2766355	An ampC-like beta-lactamase identified from Escherichia coli.	cephalosporin, penam
contig00432	2352	3656	Escherichia_coli_ampC1_beta-lactamase	0/0	100.0	96.3	FN649414.1:2765050-2766355	An ampC-like beta-lactamase identified from Escherichia coli.	cephalosporin, penam
contig00295	4611	5768	Escherichia_coli_ampH	0/0	100.0	96.7	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig00608	2061	3218	Escherichia_coli_ampH	0/0	100.0	98.9	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig00544	2032	2364	Escherichia_coli_emrE	0/0	100.0	91.9	Z11877.1:485-818	Member of the small MDR (multidrug resistance) family of transporters, in Escherichia coli this protein provides resistance against a number of positively charged compounds including ethidium bromide and erythromycin, proton-dependent secondary transporter which exchanges protons for compound translocation	macrolide
contig00214	1061	2293	Escherichia_coli_mdfA	0/0	100.0	96.0	JQ394987:0-1233	Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter.	benzalkonium_chloride, rhodamine, tetracycline
contig00048	11534	12148	evgA	0/0	100.0	99.2	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00048	12153	15746	evgS	0/0	100.0	96.6	U00096:2484373-2487967	EvgS is a sensor protein that phosphorylates the regulatory protein EvgA. evgS corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	fluoroquinolone, macrolide, penam, tetracycline
contig01640	493	1290	gadX	0/0	96.7	96.9	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig02338	1	749	gadX	0/0	90.8	100.0	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00650	417	1092	kdpE	0/0	99.7	95.3	U00096.3:721733-721055	kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding.	aminoglycoside
contig00611	507	890	marA	0/0	100.0	99.7	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00195	5799	7046	mdtA	0/0	100.0	97.4	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00858	568	1815	mdtA	0/0	100.0	100.0	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00195	2677	5799	mdtB	0/0	100.0	96.7	U00096:2155262-2158385	MdtB is a transporter that forms a heteromultimer complex with MdtC to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex.	aminocoumarin
contig00424	2994	4151	mdtE	0/0	100.0	98.5	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00424	1	2969	mdtF	0/0	95.3	98.1	U00096:3660413-3663527	MdtF is the multidrug inner membrane transporter for the MdtEF-TolC efflux complex.	fluoroquinolone, macrolide, penam
contig00310	765	1991	mdtG	0/0	100.0	97.9	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00231	2584	3792	mdtH	0/0	100.0	98.2	U00096:1125326-1124117	Multidrug resistance protein MdtH	fluoroquinolone
contig00153	7640	8671	mdtN	0/0	100.0	97.9	AP009048.1:4307588-4306556	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	acridine_dye, nucleoside
contig00312	1016	2047	mdtN	0/0	100.0	99.9	AP009048.1:4307588-4306556	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	acridine_dye, nucleoside
contig00153	5589	7640	mdtO	0/0	100.0	96.8	AP009048.1:4306557-4304505	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00312	2047	4098	mdtO	0/0	100.0	99.1	AP009048.1:4306557-4304505	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00153	4126	5592	mdtP	0/0	100.0	96.9	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00312	4095	5561	mdtP	0/0	100.0	100.0	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00261	5203	6108	mphA	0/0	100.0	99.8	D16251.1:2531-1625	The mphA gene encodes for resistance enzyme MPH(2’)-I which preferentially inactivate 14-membered macrolides (e.g.erythromycin telithromycin roxithromycin) over 16-membered macrolides (e.g.tylosin spiramycin). It phosphorylates macrolides at 2’-OH hydroxyl of desosamine sugar of macrolides in a GTP-dependent manner.	macrolide
contig00036	11294	11770	mphB	0/0	100.0	97.9	AE005174.2:3397370-3397847	The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides.	macrolide
contig00413	3033	3509	mphB	0/0	100.0	98.3	AE005174.2:3397370-3397847	The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides.	macrolide
contig01803	123	953	OXA-1	0/0	100.0	100.0	JN420336.1:2230-1399	OXA-1 is a beta-lactamase found in E. coli	cephalosporin, penam
contig00039	4694	5662	pmrF	0/0	100.0	98.0	U00096:2367070-2368039	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide
contig00841	1770	2450	QnrB5	0/0	100.0	99.1	DQ303919:0-681	QnrB5 is a plasmid-mediated quinolone resistance protein found in Salmonella enterica	fluoroquinolone
contig01015	208	864	QnrS1	0/0	100.0	100.0	DQ485529.1:0-657	QnrS1 is a plasmid-mediated quinolone resistance protein found in Shigella flexneri	fluoroquinolone
contig01317	1043	1405	ramA	0/0	96.8	90.6	JQ727668:0-375	RamA (resistance antibiotic multiple) is a positive regulator of AcrAB-TolC and leads to high level multidrug resistance in Klebsiella pneumoniae Salmonella enterica and Enterobacter aerugenes increasing the expression of both the mar operon as well as AcrAB. RamA also decreases OmpF expression.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig02102	12	827	sul2	0/0	100.0	100.0	AY055428.1:21084-20268	Sul2 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria usually found on small plasmids.	sulfonamide
contig00261	80	940	TEM-1	0/0	100.0	99.9	AL513383:161910-162771	TEM-1 is a broad-spectrum beta-lactamase found in many Gram-negative bacteria. Confers resistance to penicillins and first generation cephalosphorins.	cephalosporin, monobactam, penam, penem
contig00167	601	1847	tet(A)	0/0	97.8	99.9	AF534183.1:2970-4245	TetA is a tetracycline efflux pump found in many species of Gram-negative bacteria.	tetracycline
contig00280	1988	3193	tet(B)	0/0	100.0	99.8	AB089595:0-1206	Tet(B) is a tetracycline efflux protein expressed in many Gram-negative bacteria. It confers resistance to tetracycline doxycycline and minocycline but not tigecycline.	tetracycline
contig00185	5763	7250	tolC	0/0	100.0	98.5	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan
contig01582	1	1367	tolC	0/0	91.9	99.8	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan
contig00018	12870	14036	ugd	0/0	100.0	99.8	U00096:2099613-2098446	PmrE is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin	peptide
contig00257	4319	5962	yojI	0/0	100.0	97.3	U00096.3:2308615-2306971	YojI mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. YojI is capable of pumping out microcin molecules. The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI.	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig01776	68	904	(AGly)strB	0/0	100.0	99.9	FJ474091:264-1100	(AGly)strB	NA
contig00296	3369	4673	(Bla)AmpC1_Ecoli	0/0	100.0	99.2	FN649414:2765051-2766355	(Bla)AmpC1_Ecoli	NA
contig00432	2352	3656	(Bla)AmpC1_Ecoli	0/0	100.0	96.3	FN649414:2765051-2766355	(Bla)AmpC1_Ecoli	NA
contig00227	1151	2284	(Bla)AmpC2_Ecoli	0/0	100.0	98.0	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig01434	1	1113	(Bla)AmpC2_Ecoli	0/0	98.2	97.3	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00295	4611	5768	(Bla)ampH_Ecoli	0/0	100.0	96.7	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00608	2061	3218	(Bla)ampH_Ecoli	0/0	100.0	98.9	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00490	119	994	(Bla)blaCTX-M-15	0/0	100.0	100.0	JQ686199:261-1136	(Bla)blaCTX-M-15	NA
contig01803	123	953	(Bla)blaOXA-1	0/0	100.0	100.0	JQ682867:1-831	(Bla)blaOXA-1	NA
contig00261	80	940	(Bla)blaTEM-105	0/0	100.0	99.9	AF516720:215-1075	(Bla)blaTEM-105	NA
contig00821	1	1826	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	96.0	98.7	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA
contig01015	208	864	(Flq)qnr-S1	0/0	100.0	100.0	AB187515:9737-10393	(Flq)qnr-S1	NA
contig00841	1770	2450	(Flq)qnrB5	0/0	100.0	99.1	DQ303919:1-681	(Flq)qnrB5	NA
contig00261	5203	6108	(MLS)mph(A)	0/0	100.0	99.8	DQ445270:1626-2531	(MLS)mph(A)	NA
contig00482	221	880	(Phe)catA1	0/0	100.0	99.8	V00622:244-903	(Phe)catA1	NA
contig02102	12	827	(Sul)sul2	0/0	100.0	100.0	EU360945:1617-2432	(Sul)sul2	NA
contig00167	601	1875	(Tet)tetA	0/0	100.0	99.9	JX424423:94438-95712	(Tet)tetA	NA
contig00280	1988	3193	(Tet)tetB	0/0	100.0	99.7	AB089594:1-1206	(Tet)tetB	NA
contig01778	448	921	(Tmt)dfrA1	0/0	100.0	99.8	JQ794607:474	(Tmt)dfrA1	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig01776	68	904	aph(6)-Id	0/0	100.0	100.0	NG_047466.1	aminoglycoside O-phosphotransferase APH(6)-Id	STREPTOMYCIN
contig00490	119	994	blaCTX-M-15	0/0	100.0	100.0	NG_048935.1	class A extended-spectrum beta-lactamase CTX-M-15	CEPHALOSPORIN
contig01434	1	1113	blaEC-15	0/0	98.2	98.6	NG_049081.1	class C extended-spectrum beta-lactamase EC-15	CEPHALOSPORIN
contig00227	1151	2284	blaEC-8	0/0	100.0	98.2	NG_049086.1	cephalosporin-hydrolyzing class C beta-lactamase EC-8	CEPHALOSPORIN
contig01803	123	953	blaOXA-1	0/0	100.0	100.0	NG_049392.1	oxacillin-hydrolyzing class D beta-lactamase OXA-1	CEPHALOSPORIN
contig00261	80	940	blaTEM-1	0/0	100.0	100.0	NG_050145.1	class A broad-spectrum beta-lactamase TEM-1	BETA-LACTAM
contig00482	221	880	catA1	0/0	100.0	99.8	NG_047582.1	type A-1 chloramphenicol O-acetyltransferase	CHLORAMPHENICOL
contig01778	448	921	dfrA1	0/0	100.0	99.8	NG_047677.1	trimethoprim-resistant dihydrofolate reductase DfrA1	TRIMETHOPRIM
contig00261	5187	6108	mph(A)	1/1	100.0	99.5	NG_047986.1	Mph(A) family macrolide 2’-phosphotransferase	MACROLIDE
contig00841	1806	2450	qnrB19	0/0	100.0	100.0	NG_050479.1	quinolone resistance pentapeptide repeat protein QnrB19	QUINOLONE
contig01015	208	864	qnrS1	0/0	100.0	100.0	NG_050543.1	quinolone resistance pentapeptide repeat protein QnrS1	QUINOLONE
contig02102	12	827	sul2	0/0	100.0	100.0	NG_051852.1	sulfonamide-resistant dihydropteroate synthase Sul2	SULFONAMIDE
contig00167	676	1875	tet(A)	0/0	100.0	99.9	NG_048154.1	tetracycline efflux MFS transporter Tet(A)	TETRACYCLINE
contig00280	1988	3193	tet(B)	0/0	100.0	100.0	NG_048163.1	tetracycline efflux MFS transporter Tet(B)	TETRACYCLINE

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00136	19	1176	ACRE	0/0	100.0	98.8	MEG_408	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRE	NA
contig00136	1188	4292	ACRF	0/0	100.0	98.0	MEG_409	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRF	NA
contig00963	1383	2045	ACRS	0/0	100.0	97.1	MEG_415	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS	NA
contig01390	771	1433	ACRS	0/0	100.0	99.1	MEG_415	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS	NA
contig00295	4611	5768	AMPH	0/0	100.0	96.7	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00608	2061	3218	AMPH	0/0	100.0	98.9	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig01776	68	904	APH6	0/0	100.0	100.0	MEG_1084	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH6	NA
contig00014	1070	2923	ASMA	0/0	100.0	97.3	MEG_1180	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:ASMA	NA
contig00057	6850	7669	BACA	0/0	99.8	97.6	MEG_1189	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00707	1993	2814	BACA	0/0	100.0	99.6	MEG_1189	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00243	4090	5280	BCR	0/0	100.0	97.1	MEG_1210	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR	NA
contig00227	1151	2284	BLAEC	0/0	100.0	98.2	MEG_1278	Drugs:betalactams:Class_C_betalactamases:BLAEC	NA
contig01434	1	1113	BLAEC	0/0	98.2	98.6	MEG_1282	Drugs:betalactams:Class_C_betalactamases:BLAEC	NA
contig00482	210	880	CATA	0/0	100.0	100.0	MEG_1593	Drugs:Phenicol:Chloramphenicol_acetyltransferases:CATA	NA
contig01049	330	1703	CPXAR	0/0	100.0	98.1	MEG_2121	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00128	1060	1692	CRP	0/0	100.0	99.0	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00503	2122	3062	CTX	0/0	99.8	91.7	MEG_2435	Drugs:betalactams:Class_A_betalactamases:CTX	NA
contig01778	448	921	DFRA	0/0	100.0	99.8	MEG_2528	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00817	947	2485	EMRB	0/0	100.0	98.2	MEG_2725	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRB	NA
contig00716	1307	2497	EMRD	0/0	100.0	98.1	MEG_2729	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD	NA
contig01494	401	1489	EMRD	0/0	91.4	99.7	MEG_2729	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD	NA
contig00048	9955	11118	EMRK	0/0	100.0	97.2	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig00176	91	1254	EMRK	0/0	100.0	99.8	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig01534	47	577	EMRR	0/0	100.0	99.4	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig01729	37	567	EMRR	0/0	100.0	100.0	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00048	8417	9955	EMRY	0/0	100.0	97.5	MEG_2736	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRY	NA
contig00176	1254	2792	EMRY	0/0	100.0	99.1	MEG_2736	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRY	NA
contig00048	12153	15746	EVGS	0/0	100.0	98.0	MEG_2869	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EVGS	NA
contig01640	493	1290	GADX	0/0	96.7	96.9	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig02338	1	749	GADX	0/0	90.8	100.0	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00650	417	1092	KDPE	0/0	99.7	95.3	MEG_3448	Drugs:Aminoglycosides:Aminoglycoside_efflux_pumps:KDPE	NA
contig00611	501	890	MARA	0/0	100.0	99.7	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00611	53	487	MARR	0/0	100.0	98.4	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00214	1061	2293	MDFA	0/0	100.0	97.7	MEG_3737	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDFA	NA
contig00195	5799	7046	MDTA	0/0	100.0	97.4	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00858	568	1815	MDTA	0/0	100.0	100.0	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00195	2677	5799	MDTB	0/0	100.0	96.7	MEG_3747	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTB	NA
contig00424	2994	4151	MDTE	0/0	100.0	98.5	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00424	1	2969	MDTF	0/0	95.3	98.1	MEG_3752	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTF	NA
contig00310	765	1991	MDTG	0/0	100.0	98.1	MEG_3753	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig00231	2584	3792	MDTH	0/0	100.0	98.2	MEG_3755	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTH	NA
contig01165	1328	1657	MDTI	0/0	100.0	99.7	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00645	2792	3157	MDTJ	0/0	100.0	99.5	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00153	7640	8671	MDTN	0/0	100.0	97.9	MEG_3763	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN	NA
contig00312	1016	2047	MDTN	0/0	100.0	99.9	MEG_3763	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN	NA
contig00153	5589	7640	MDTO	0/0	100.0	96.8	MEG_3764	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTO	NA
contig00312	2047	4098	MDTO	0/0	100.0	99.1	MEG_3764	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTO	NA
contig00153	4126	5592	MDTP	0/0	100.0	96.9	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig00312	4095	5561	MDTP	0/0	100.0	100.0	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig00261	5187	6108	MPHA	1/1	100.0	99.5	MEG_4030	Drugs:MLS:Macrolide_phosphotransferases:MPHA	NA
contig00036	11294	11770	MPHB	0/0	100.0	97.9	MEG_4033	Drugs:MLS:Macrolide_phosphotransferases:MPHB	NA
contig00413	3033	3509	MPHB	0/0	100.0	98.3	MEG_4033	Drugs:MLS:Macrolide_phosphotransferases:MPHB	NA
contig00544	2032	2364	MVRC	0/0	100.0	91.9	MEG_4103	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MVRC	NA
contig01803	123	953	OXA	0/0	100.0	100.0	MEG_4980	Drugs:betalactams:Class_D_betalactamases:OXA	NA
contig00821	1	1826	PBP2	0/0	96.0	98.7	MEG_5400	Drugs:betalactams:Penicillin_binding_protein:PBP2	NA
contig00296	3369	4673	PBP4B	0/0	100.0	99.2	MEG_5409	Drugs:betalactams:Penicillin_binding_protein:PBP4B	NA
contig00432	2352	3656	PBP4B	0/0	100.0	96.3	MEG_5409	Drugs:betalactams:Penicillin_binding_protein:PBP4B	NA
contig00039	4694	5662	PMRF	0/0	100.0	98.0	MEG_5801	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF	NA
contig00841	1770	2450	QNRB	0/0	100.0	99.1	MEG_5930	Drugs:Fluoroquinolones:Quinolone_resistance_protein_Qnr:QNRB	NA
contig01015	208	864	QNRS	0/0	100.0	100.0	MEG_6020	Drugs:Fluoroquinolones:Quinolone_resistance_protein_Qnr:QNRS	NA
contig01317	1043	1405	RAMA	0/0	96.8	90.6	MEG_6044	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:RAMA	NA
contig00193	2369	3238	ROBA	0/0	100.0	99.3	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00685	1730	2052	SOXS	0/0	99.7	98.1	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00735	1552	1874	SOXS	0/0	99.7	99.7	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig02102	12	827	SULII	0/0	100.0	100.0	MEG_6617	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULII	NA
contig00261	62	1307	TEM	0/0	98.3	99.4	MEG_6875	Drugs:betalactams:Class_A_betalactamases:TEM	NA
contig00167	601	1875	TETA	0/0	100.0	99.9	MEG_7024	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETA	NA
contig00280	1988	3193	TETB	0/0	100.0	100.0	MEG_7052	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETB	NA
contig00280	3987	4403	TETD	0/0	100.0	100.0	MEG_7070	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETD	NA
contig00018	12870	14036	UGD	0/0	100.0	99.8	MEG_7328	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:UGD	NA
contig00257	4319	5962	YOGI	0/0	100.0	97.3	MEG_7842	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:YOGI	NA

ORTHO013EI

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00238	1696	2556	aac(3)-IIa_1	0/0	100	99.8	X51534	aac(3)-IIa	Gentamicin, Tobramycin
contig00257	1540	2139	aac(6’)-Ib-cr_1	0/0	100	100.0	DQ303918	aac(6’)-Ib-cr	Ciprofloxacin
contig00020	32083	33228	blaACT-6_1	0/0	100	91.9	FJ237366	blaACT-6
contig00102	2637	3512	blaCTX-M-15_1	0/0	100	100.0	AY044436	blaCTX-M-15	Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig00257	579	1409	blaOXA-1_1	0/0	100	100.0	HQ170510	blaOXA-1	Amoxicillin, Amoxicillin+Clavulanic_acid, Ampicillin, Ampicillin+Clavulanic_acid, Cefepime, Piperacillin, Piperacillin+Tazobactam
contig00033	14306	15166	blaTEM-1A_1	0/0	100	100.0	HM749966	blaTEM-1A	Amoxicillin, Ampicillin, Cephalothin, Piperacillin, Ticarcillin
contig00033	5970	6443	dfrA15_2	0/0	100	100.0	AF221900	dfrA15	Trimethoprim
contig00189	3188	3613	fosA_1	0/0	100	96.0	M85195	fosA	Fosfomycin
contig00116	4402	5046	qnrB1_1	0/0	100	100.0	DQ351241	qnrB1	Ciprofloxacin
contig00033	3733	4599	sul1_5	0/0	100	99.8	EU780013	sul1	Sulfamethoxazole

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00238	1696	2556	AAC(3)-IIe	0/0	100.0	99.5	EU022315.1:0-861	AAC(3)-IIe is a plasmid-encoded aminoglycoside acetyltransferase in E. coli	aminoglycoside
contig00257	1540	2139	AAC(6’)-Ib-cr	0/0	100.0	100.0	DQ303918:0-600	AAC(6’)-Ib-cr is an aminoglycoside acetyltransferase encoded by plasmids transposons integrons in Enterobacteriaceae. The aac(6’)-Ib-cr variant gene can induce resistance against aminoglycoside and fluoroquinolone simultaneously	aminoglycoside, fluoroquinolone
contig00020	32083	33228	ACT-6	0/0	100.0	91.9	FJ237366:40-1186	ACT-6 is a beta-lactamase found in Klebsiella pneumoniae	carbapenem, cephalosporin, cephamycin, penam
contig00102	2637	3512	CTX-M-15	0/0	100.0	100.0	AY044436:1435-2311	CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family	cephalosporin
contig00033	5970	6443	dfrA15	0/0	100.0	100.0	KF534911:39-513	dfrA15 is an integron-encoded dihydrofolate reductase found in Vibrio cholerae	diaminopyrimidine
contig00074	14652	15845	Enterobacter_cloacae_acrA	0/0	100.0	94.0	DQ679966:299-1493	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. cloacae.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00189	3188	3613	FosA2	0/0	100.0	91.8	EU487198:216-642	An enzyme that confers resistance to fosfomycin in Enterobacter cloacae by breaking the epoxide ring of the molecule. It depends on the cofactors Manganese (II) and Potassium and uses Glutathione (GSH) as the nucleophilic molecule.	fosfomycin
contig00257	579	1409	OXA-1	0/0	100.0	100.0	JN420336.1:2230-1399	OXA-1 is a beta-lactamase found in E. coli	cephalosporin, penam
contig00116	4366	5046	QnrB17	0/0	100.0	99.1	AM919398:0-681	QnrB17 is a plasmid-mediated quinolone resistance protein found in Citrobacter freundii	fluoroquinolone
contig00160	4065	4416	ramA	0/0	93.9	90.9	JQ727668:0-375	RamA (resistance antibiotic multiple) is a positive regulator of AcrAB-TolC and leads to high level multidrug resistance in Klebsiella pneumoniae Salmonella enterica and Enterobacter aerugenes increasing the expression of both the mar operon as well as AcrAB. RamA also decreases OmpF expression.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00033	3733	4572	sul1	0/0	100.0	99.9	JF969163:1053-1893	Sul1 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria. It is linked to other resistance genes of class 1 integrons.	sulfonamide
contig00033	14306	15166	TEM-150	0/0	100.0	99.9	AM183304:208-1069	TEM-150 is a beta-lactamase found in Enterobacter spp. E. coli and Klebsiella pneumoniae.	cephalosporin, monobactam, penam, penem

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00238	1696	2556	(AGly)aac3-IIa	0/0	100.0	99.8	X51534:91-951	(AGly)aac3-IIa	NA
contig00033	5077	5878	(AGly)aadA1-pm	0/0	96.5	99.9	JQ690540:7968-8798	(AGly)aadA1-pm	NA
contig00020	32083	33228	(Bla)blaACT-6	0/0	100.0	91.9	FJ237366:41-1186	(Bla)blaACT-6	NA
contig00102	2637	3512	(Bla)blaCTX-M-15	0/0	100.0	100.0	JQ686199:261-1136	(Bla)blaCTX-M-15	NA
contig00257	579	1409	(Bla)blaOXA-1	0/0	100.0	100.0	JQ682867:1-831	(Bla)blaOXA-1	NA
contig00033	14306	15166	(Bla)blaTEM-150	0/0	100.0	99.9	AM183304:209-1069	(Bla)blaTEM-150	NA
contig00189	3188	3613	(Fcyn)FosA2	0/0	100.0	91.8	EU487198:217-642	(Fcyn)FosA2	NA
contig00116	4366	5046	(Flq)qnrB1	0/0	100.0	99.8	DQ351241:1-681	(Flq)qnrB1	NA
contig00033	3733	4572	(Sul)sul1	0/0	100.0	99.9	AF071413:6700-7539	(Sul)sul1	NA
contig00033	5970	6443	(Tmt)dfrA15b	0/0	100.0	99.2	AJ867237:177-650	(Tmt)dfrA15b	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00238	1696	2556	aac(3)-IIe	0/0	100	99.8	NG_047244.1	aminoglycoside N-acetyltransferase AAC(3)-IIe	GENTAMICIN
contig00257	1540	2094	aac(6’)-Ib-D181Y	0/0	100	99.8	NG_067946.1	AAC(6’)-Ib family aminoglycoside 6’-N-acetyltransferase	AMIKACIN, KANAMYCIN, TOBRAMYCIN
contig00033	5077	5868	aadA1	0/0	100	99.9	NG_052266.1	ANT(3’’)-Ia family aminoglycoside nucleotidyltransferase AadA1	STREPTOMYCIN
contig00020	32083	33228	blaACT-63	0/0	100	99.4	NG_061406.1	cephalosporin-hydrolyzing class C beta-lactamase ACT-63	CEPHALOSPORIN
contig00102	2637	3512	blaCTX-M-15	0/0	100	100.0	NG_048935.1	class A extended-spectrum beta-lactamase CTX-M-15	CEPHALOSPORIN
contig00257	579	1409	blaOXA-1	0/0	100	100.0	NG_049392.1	oxacillin-hydrolyzing class D beta-lactamase OXA-1	CEPHALOSPORIN
contig00033	14306	15166	blaTEM-150	0/0	100	99.9	NG_050194.1	class A beta-lactamase TEM-150	BETA-LACTAM
contig00033	5970	6443	dfrA15	0/0	100	100.0	NG_047702.1	trimethoprim-resistant dihydrofolate reductase DfrA15	TRIMETHOPRIM
contig00189	3188	3613	fosA	0/0	100	96.0	NG_050405.1	fosfomycin resistance glutathione transferase FosA	FOSFOMYCIN
contig00116	4402	5046	qnrB1	0/0	100	100.0	NG_050469.1	quinolone resistance pentapeptide repeat protein QnrB1	QUINOLONE
contig00033	3733	4572	sul1	0/0	100	99.9	NG_048082.1	sulfonamide-resistant dihydropteroate synthase Sul1	SULFONAMIDE

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00238	1696	2556	AAC3	0/0	100.0	99.8	MEG_44	Drugs:Aminoglycosides:Aminoglycoside_N-acetyltransferases:AAC3	NA
contig00074	14652	15845	ACRB	0/0	100.0	94.0	MEG_402	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRB	NA
contig00020	32083	33228	ACT	0/0	100.0	99.3	MEG_440	Drugs:betalactams:Class_C_betalactamases:ACT	NA
contig00033	5077	5878	ANT3-DPRIME	0/0	96.5	99.9	MEG_915	Drugs:Aminoglycosides:Aminoglycoside_O-nucleotidyltransferases:ANT3-DPRIME	NA
contig00033	5970	6443	DFRA	0/0	100.0	99.4	MEG_2492	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00189	3032	3613	FOSA	0/0	100.0	92.4	MEG_2990	Drugs:Fosfomycin:Fosfomycin_thiol_transferases:FOSA	NA
contig00257	579	1409	OXA	0/0	100.0	100.0	MEG_4980	Drugs:betalactams:Class_D_betalactamases:OXA	NA
contig00116	4366	5046	QNRB	0/0	100.0	99.1	MEG_5928	Drugs:Fluoroquinolones:Quinolone_resistance_protein_Qnr:QNRB	NA
contig00160	4065	4416	RAMA	0/0	93.9	90.9	MEG_6044	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:RAMA	NA
contig00033	3606	4573	SULI	0/0	100.0	99.9	MEG_6615	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULI	NA
contig00033	14288	15533	TEM	0/0	98.3	99.5	MEG_6875	Drugs:betalactams:Class_A_betalactamases:TEM	NA

ORTHO055E

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00002	1695	2555	aac(3)-IIa_1	0/0	100	99.8	X51534	aac(3)-IIa	Gentamicin, Tobramycin
contig00425	563	1438	blaCTX-M-15_1	0/0	100	100.0	AY044436	blaCTX-M-15	Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig00491	1692	2111	fosA_6	0/0	100	95.0	ACZD01000244	fosA	Fosfomycin
contig00015	5873	7048	oqxA_1	0/0	100	99.4	EU370913	oqxA	Nalidixic_acid, Ciprofloxacin
contig00015	2697	5849	oqxB_1	0/0	100	95.3	EU370913	oqxB	Nalidixic_acid, Ciprofloxacin

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00002	1695	2555	AAC(3)-IIe	0/0	100.0	99.5	EU022315.1:0-861	AAC(3)-IIe is a plasmid-encoded aminoglycoside acetyltransferase in E. coli	aminoglycoside
contig00425	563	1438	CTX-M-15	0/0	100.0	100.0	AY044436:1435-2311	CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family	cephalosporin
contig00491	1692	2111	FosA5	0/0	100.0	94.5	KP143090.1:1619-1199	fosA5 is a fosfomycin resistance gene isolated from clinical strain of Escherichia coli E265. It is susceptible to amikacin tetracycline and imipenem and resistant to sulphonamide cephalosporins gentamicin ciprofloxacin chloramphenicol and streptomycin	fosfomycin
contig00029	8174	9367	Klebsiella_pneumoniae_acrA	2/3	99.8	94.8	AJ318073.1:793-1990	AcrA is a subunit of the AcrAB multidrug efflux system that in K. pneumoniae which is encoded by the acrRAB operon.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00278	2116	2445	Klebsiella_pneumoniae_KpnF	0/0	100.0	93.3	AP006725.1:2484238-2484568	KpnF subunit of KpnEF resembles EbrAB from E. coli. Mutation in KpnEF resulted in increased susceptibility to cefepime ceftriaxon colistin erythromycin rifampin tetracycline and streptomycin as well as enhanced sensitivity toward sodium dodecyl sulfate deoxycholate dyes benzalkonium chloride chlorhexidine and triclosan.	aminoglycoside, cephalosporin, macrolide, peptide, rifamycin, tetracycline
contig00259	3996	5168	Klebsiella_pneumoniae_KpnG	0/0	100.0	94.6	ACWO01000051.1:22092-23265	KpnG consists of ~390 residues and resembles EmrA of E. coli. Disruption of the pump components KpnG-KpnH signficantly decrease resistance to azithromycin ceftazidime ciprofloxacin ertapenem erythromycin gentamicin imipenem ticarcillin norfloxacin polymyxin-B piperacillin spectinomycin tobramycin and streptomycin	aminoglycoside, carbapenem, cephalosporin, fluoroquinolone, macrolide, penam, penem, peptide
contig00015	5873	7048	oqxA	0/0	100.0	99.4	EU370913.1:46651-47827	RND efflux pump conferring resistance to fluoroquinolone	diaminopyrimidine, fluoroquinolone, glycylcycline, nitrofuran, tetracycline
contig00015	2697	5849	oqxB	0/0	100.0	95.3	EU370913.1:47850-51003	RND efflux pump conferring resistance to fluoroquinolone	diaminopyrimidine, fluoroquinolone, glycylcycline, nitrofuran, tetracycline

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00002	1695	2555	(AGly)aac3-IIa	0/0	100	99.8	X51534:91-951	(AGly)aac3-IIa	NA
contig00149	5314	6474	(Bla)ampH	0/0	100	96.0	CP003785:4208384-4209544	(Bla)ampH	NA
contig00425	563	1438	(Bla)blaCTX-M-15	0/0	100	100.0	JQ686199:261-1136	(Bla)blaCTX-M-15	NA
contig00491	1692	2111	(Fcyn)FosA5	0/0	100	94.5	KP143090:1200-1619	(Fcyn)FosA5	NA
contig00015	5873	7048	(Flq)OqxA	0/0	100	99.4	EU370913:46652-47827	(Flq)OqxA	NA
contig00015	2697	5849	(Flq)OqxBgb	0/0	100	95.3	EU370913:47851-51003	(Flq)OqxBgb	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00002	1695	2555	aac(3)-IIe	0/0	100	99.8	NG_047244.1	aminoglycoside N-acetyltransferase AAC(3)-IIe	GENTAMICIN
contig00425	563	1438	blaCTX-M-15	0/0	100	100.0	NG_048935.1	class A extended-spectrum beta-lactamase CTX-M-15	CEPHALOSPORIN
contig00491	1692	2111	fosA_gen	0/0	100	95.0	NG_047881.1	FosA family fosfomycin resistance glutathione transferase	FOSFOMYCIN
contig00015	5873	7048	oqxA9	0/0	100	99.8	NG_050427.1	multidrug efflux RND transporter periplasmic adaptor subunit OqxA9	PHENICOL, QUINOLONE
contig00015	2697	5849	oqxB11	0/0	100	95.9	NG_050429.1	multidrug efflux RND transporter permease subunit OqxB11	PHENICOL, QUINOLONE

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00002	1695	2555	AAC3	0/0	100.0	99.8	MEG_44	Drugs:Aminoglycosides:Aminoglycoside_N-acetyltransferases:AAC3	NA
contig00029	8174	9367	ACRA	2/3	99.8	94.8	MEG_400	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00149	5314	6474	AMPH	0/0	100.0	96.0	MEG_730	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00114	1710	3533	ASMA	0/0	100.0	93.2	MEG_1179	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:ASMA	NA
contig00010	18800	19498	CPXAR	0/0	100.0	96.8	MEG_2116	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00010	19495	20868	CPXAR	0/0	100.0	95.6	MEG_2115	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00491	1692	2111	FOSA	0/0	100.0	95.0	MEG_2991	Drugs:Fosfomycin:Fosfomycin_thiol_transferases:FOSA	NA
contig00005	38583	39814	KDEA	0/0	99.9	94.2	MEG_3447	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:KDEA	NA
contig00259	3996	5168	KPN	0/0	100.0	94.6	MEG_3512	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:KPN	NA
contig00278	2116	2445	KPNF	0/0	100.0	93.3	MEG_3515	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:KPNF	NA
contig00062	18258	19361	KPNO	4/18	99.5	94.5	MEG_3516	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:KPNO	NA
contig00015	5873	7048	OQXA	0/0	100.0	99.8	MEG_4331	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:OQXA	NA
contig00015	2697	5849	OQXB	0/0	100.0	95.9	MEG_4364	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:OQXB	NA
contig00115	5506	6972	PHOR	0/0	100.0	93.5	MEG_5786	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_regulator:PHOR	NA

ORTHO082EI

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00109	1799	2329	aac(3)-Ib_1	0/0	100.0	100.0	L06157	aac(3)-Ib	Gentamicin
contig00073	6087	6947	aac(3)-IId_1	0/0	100.0	99.9	EU022314	aac(3)-IId	Gentamicin, Tobramycin
contig00113	1538	2137	aac(6’)-Ib-cr_1	0/0	100.0	100.0	DQ303918	aac(6’)-Ib-cr	Ciprofloxacin
contig00082	1656	2457	aadA2_1	0/0	97.9	99.9	NC_010870	aadA2	Streptomycin
contig00052	13755	14900	blaCMY-135_1	0/0	100.0	99.7	KP981366	blaCMY-135	Amoxicillin, Amoxicillin+Clavulanic_acid, Ampicillin, Ampicillin+Clavulanic_acid, Cefotaxime, Cefoxitin, Ceftazidime, Piperacillin, Piperacillin+Tazobactam, Ticarcillin, Ticarcillin+Clavulanic_acid
contig00015	107313	108188	blaCTX-M-15_1	0/0	100.0	100.0	AY044436	blaCTX-M-15	Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig00113	577	1407	blaOXA-1_1	0/0	100.0	100.0	HQ170510	blaOXA-1	Amoxicillin, Amoxicillin+Clavulanic_acid, Ampicillin, Ampicillin+Clavulanic_acid, Cefepime, Piperacillin, Piperacillin+Tazobactam
contig00109	854	1681	blaOXA-2_1	0/0	100.0	100.0	DQ112222	blaOXA-2	Amoxicillin, Amoxicillin+Clavulanic_acid, Ampicillin, Ampicillin+Clavulanic_acid, Ceftazidime, Piperacillin
contig00073	255	1115	blaTEM-1B_1	0/0	100.0	100.0	AY458016	blaTEM-1B	Amoxicillin, Ampicillin, Cephalothin, Piperacillin, Ticarcillin
contig00141	350	1000	catA1_1	0/0	98.6	99.8	V00622	catA1	Chloramphenicol
contig00082	2855	3352	dfrA12_8	0/0	100.0	100.0	AM040708	dfrA12	Trimethoprim
contig00137	442	924	dfrA14_5	0/0	100.0	99.6	DQ388123	dfrA14	Trimethoprim
contig00139	69	990	mph(A)_2	1/1	100.0	99.7	U36578	mph(A)	Erythromycin, Azithromycin, Spiramycin, Telithromycin
contig00075	4401	5045	qnrB1_1	0/0	100.0	100.0	DQ351241	qnrB1	Ciprofloxacin
contig00082	312	1178	sul1_5	0/0	100.0	99.9	EU780013	sul1	Sulfamethoxazole
contig00083	2980	3795	sul2_2	0/0	100.0	100.0	AY034138	sul2	Sulfamethoxazole
contig00088	1427	2695	tet(A)_6	1/22	97.8	93.2	AF534183	tet(A)	Doxycycline, Tetracycline
contig00093	1638	2822	tet(D)_1	0/0	100.0	100.0	AF467077	tet(D)	Doxycycline, Tetracycline

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00109	1799	2329	AAC(3)-Ib	0/0	100.0	100.0	L06157:554-1085	AAC(3)-Ib is an integron-encoded aminoglycoside acetyltransferase in P. aeruginosa	aminoglycoside
contig00073	6087	6947	AAC(3)-IId	0/0	100.0	99.9	EU022314.1:0-861	AAC(3)-IId is a plasmid-encoded aminoglycoside acetyltransferase in E. coli	aminoglycoside
contig00113	1538	2137	AAC(6’)-Ib-cr	0/0	100.0	100.0	DQ303918:0-600	AAC(6’)-Ib-cr is an aminoglycoside acetyltransferase encoded by plasmids transposons integrons in Enterobacteriaceae. The aac(6’)-Ib-cr variant gene can induce resistance against aminoglycoside and fluoroquinolone simultaneously	aminoglycoside, fluoroquinolone
contig00082	1656	2435	aadA2	0/0	100.0	99.9	AF156486:5012-5792	aadA2 is an aminoglycoside nucleotidyltransferase gene encoded by plasmids and integrons in K. pneumoniae Salmonella spp. Corynebacterium glutamicum C. freundii and Aeromonas spp.	aminoglycoside
contig00141	350	1000	catI	0/0	98.6	99.8	V00622:243-903	catI is a chromosome and transposon-encoded variant of the cat gene found in Escherichia coli and Acinetobacter baumannii	phenicol
contig00052	13755	14900	CMY-135	0/0	100.0	99.7	KP981366.1:0-1146	CMY-135 is a class C beta-lactamase that confers resistance to cephamycin.	cephamycin
contig00015	107313	108188	CTX-M-15	0/0	100.0	100.0	AY044436:1435-2311	CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family	cephalosporin
contig00082	2855	3352	dfrA12	0/0	100.0	100.0	GU585907.1:22103-21605	dfrA12 is an integron-encoded dihydrofolate reductase found in Vibrio cholerae	diaminopyrimidine
contig00137	442	924	dfrA14	0/0	100.0	99.8	EU780012:2162-2645	dfrA14 is an integron-encoded dihydrofolate reductase found in Escherichia coli	diaminopyrimidine
contig00014	49710	50123	H-NS	0/0	100.0	90.3	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00139	69	974	mphA	0/0	100.0	100.0	D16251.1:2531-1625	The mphA gene encodes for resistance enzyme MPH(2’)-I which preferentially inactivate 14-membered macrolides (e.g.erythromycin telithromycin roxithromycin) over 16-membered macrolides (e.g.tylosin spiramycin). It phosphorylates macrolides at 2’-OH hydroxyl of desosamine sugar of macrolides in a GTP-dependent manner.	macrolide
contig00113	577	1407	OXA-1	0/0	100.0	100.0	JN420336.1:2230-1399	OXA-1 is a beta-lactamase found in E. coli	cephalosporin, penam
contig00109	854	1681	OXA-2	0/0	100.0	100.0	M95287.4:2455-3283	OXA-2 is a beta-lactamase found in the Enterobacteriaceae family.	carbapenem, cephalosporin, penam
contig00109	60	392	qacH	0/0	100.0	99.4	DQ149925.1:188-521	qacH is a subunit of the qac multidrug efflux pump in Vibrio cholerae	fluoroquinolone
contig00075	4364	5045	QnrB17	1/1	100.0	99.1	AM919398:0-681	QnrB17 is a plasmid-mediated quinolone resistance protein found in Citrobacter freundii	fluoroquinolone
contig00082	312	1151	sul1	0/0	100.0	100.0	JF969163:1053-1893	Sul1 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria. It is linked to other resistance genes of class 1 integrons.	sulfonamide
contig00083	2980	3795	sul2	0/0	100.0	100.0	AY055428.1:21084-20268	Sul2 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria usually found on small plasmids.	sulfonamide
contig00073	255	1115	TEM-1	0/0	100.0	99.9	AL513383:161910-162771	TEM-1 is a broad-spectrum beta-lactamase found in many Gram-negative bacteria. Confers resistance to penicillins and first generation cephalosphorins.	cephalosporin, monobactam, penam, penem
contig00088	1427	2695	tet(A)	1/22	97.8	93.2	AF534183.1:2970-4245	TetA is a tetracycline efflux pump found in many species of Gram-negative bacteria.	tetracycline
contig00093	1638	2822	tet(D)	0/0	100.0	100.0	AF467077.1:163-1348	TetD is a tetracycline efflux pump found exclusively in Gram-negative bacteria.	tetracycline

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00109	1799	2329	(AGly)aac3-Ib	0/0	100.0	100.0	L06157:555-1085	(AGly)aac3-Ib	NA
contig00073	6087	6947	(AGly)aac3-IId	0/0	100.0	99.9	EU022314:1-861	(AGly)aac3-IId	NA
contig00144	126	922	(AGly)aadA1-pm	0/0	95.9	99.9	JQ690540:7968-8798	(AGly)aadA1-pm	NA
contig00082	1656	2435	(AGly)aadA2	0/0	100.0	99.9	X68227:66-945	(AGly)aadA2	NA
contig00052	13755	14900	(Bla)blaCMY-135	0/0	100.0	99.7	KP981366:1-1146	(Bla)blaCMY-135	NA
contig00015	107313	108188	(Bla)blaCTX-M-15	0/0	100.0	100.0	JQ686199:261-1136	(Bla)blaCTX-M-15	NA
contig00113	577	1407	(Bla)blaOXA-1	0/0	100.0	100.0	JQ682867:1-831	(Bla)blaOXA-1	NA
contig00109	854	1681	(Bla)blaOXA-2	0/0	100.0	100.0	HM131431:1-828	(Bla)blaOXA-2	NA
contig00073	255	1115	(Bla)blaTEM-105	0/0	100.0	99.9	AF516720:215-1075	(Bla)blaTEM-105	NA
contig00075	4364	5045	(Flq)qnrB1	1/1	100.0	99.8	DQ351241:1-681	(Flq)qnrB1	NA
contig00139	69	974	(MLS)mph(A)	0/0	100.0	100.0	DQ445270:1626-2531	(MLS)mph(A)	NA
contig00141	350	1000	(Phe)catA1	0/0	98.6	99.8	V00622:244-903	(Phe)catA1	NA
contig00082	312	1151	(Sul)sul1	0/0	100.0	100.0	AF071413:6700-7539	(Sul)sul1	NA
contig00083	2980	3795	(Sul)sul2	0/0	100.0	100.0	EU360945:1617-2432	(Sul)sul2	NA
contig00088	1427	2723	(Tet)tetA	1/22	100.0	93.3	JX424423:94438-95712	(Tet)tetA	NA
contig00093	1638	2822	(Tet)tetD	0/0	100.0	100.0	AB089602:1521-2705	(Tet)tetD	NA
contig00088	755	1396	(Tet)tetR	1/9	98.6	93.1	HF545434:53576-54226	(Tet)tetR	NA
contig00082	2855	3352	(Tmt)dfrA12	0/0	100.0	100.0	Z21672:310-807	(Tmt)dfrA12	NA
contig00137	442	915	(Tmt)dfrA14	0/0	100.0	100.0	GU726917:72-545	(Tmt)dfrA14	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00109	1799	2263	aac(3)-Ib	0/0	100.0	100.0	NG_047257.1	aminoglycoside N-acetyltransferase AAC(3)-Ib	GENTAMICIN
contig00073	6087	6947	aac(3)-IId	0/0	100.0	100.0	NG_047251.1	aminoglycoside N-acetyltransferase AAC(3)-IId	GENTAMICIN
contig00113	1538	2092	aac(6’)-Ib-D181Y	0/0	100.0	99.8	NG_067946.1	AAC(6’)-Ib family aminoglycoside 6’-N-acetyltransferase	AMIKACIN, KANAMYCIN, TOBRAMYCIN
contig00144	126	917	aadA1	0/0	100.0	100.0	NG_052536.1	ANT(3’’)-Ia family aminoglycoside nucleotidyltransferase AadA1	STREPTOMYCIN
contig00082	1656	2447	aadA2	0/0	100.0	100.0	NG_047343.1	ANT(3’’)-Ia family aminoglycoside nucleotidyltransferase AadA2	STREPTOMYCIN
contig00052	13755	14900	blaCMY-135	0/0	100.0	99.7	NG_048805.1	class C beta-lactamase CMY-135	CEPHALOSPORIN
contig00015	107313	108188	blaCTX-M-15	0/0	100.0	100.0	NG_048935.1	class A extended-spectrum beta-lactamase CTX-M-15	CEPHALOSPORIN
contig00113	577	1407	blaOXA-1	0/0	100.0	100.0	NG_049392.1	oxacillin-hydrolyzing class D beta-lactamase OXA-1	CEPHALOSPORIN
contig00109	854	1681	blaOXA-2	0/0	100.0	100.0	NG_049496.1	oxacillin-hydrolyzing class D beta-lactamase OXA-2	BETA-LACTAM
contig00073	255	1115	blaTEM-1	0/0	100.0	100.0	NG_050145.1	class A broad-spectrum beta-lactamase TEM-1	BETA-LACTAM
contig00141	350	1000	catA1	0/0	98.6	99.8	NG_047582.1	type A-1 chloramphenicol O-acetyltransferase	CHLORAMPHENICOL
contig00082	2855	3352	dfrA12	0/0	100.0	100.0	NG_047689.1	trimethoprim-resistant dihydrofolate reductase DfrA12	TRIMETHOPRIM
contig00137	442	915	dfrA14	0/0	100.0	100.0	NG_056035.1	trimethoprim-resistant dihydrofolate reductase DfrA14	TRIMETHOPRIM
contig00139	69	990	mph(A)	1/1	100.0	99.7	NG_047986.1	Mph(A) family macrolide 2’-phosphotransferase	MACROLIDE
contig00075	4401	5045	qnrB1	0/0	100.0	100.0	NG_050469.1	quinolone resistance pentapeptide repeat protein QnrB1	QUINOLONE
contig00082	312	1151	sul1	0/0	100.0	100.0	NG_048082.1	sulfonamide-resistant dihydropteroate synthase Sul1	SULFONAMIDE
contig00083	2980	3795	sul2	0/0	100.0	100.0	NG_051852.1	sulfonamide-resistant dihydropteroate synthase Sul2	SULFONAMIDE
contig00088	1524	2723	tet(A)	0/0	100.0	100.0	NG_048157.1	tetracycline efflux MFS transporter Tet(A)	TETRACYCLINE
contig00093	1638	2822	tet(D)	0/0	100.0	99.9	NG_048184.1	tetracycline efflux MFS transporter Tet(D)	TETRACYCLINE

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00073	6087	6947	AAC3	0/0	100.0	100.0	MEG_64	Drugs:Aminoglycosides:Aminoglycoside_N-acetyltransferases:AAC3	NA
contig00109	1799	2329	AAC3-PRIME	0/0	100.0	100.0	MEG_69	Drugs:Aminoglycosides:Aminoglycoside_N-acetyltransferases:AAC3-PRIME	NA
contig00082	1656	2457	ANT3-DPRIME	0/0	97.9	99.9	MEG_975	Drugs:Aminoglycosides:Aminoglycoside_O-nucleotidyltransferases:ANT3-DPRIME	NA
contig00144	126	922	ANT3-DPRIME	0/0	95.9	99.9	MEG_915	Drugs:Aminoglycosides:Aminoglycoside_O-nucleotidyltransferases:ANT3-DPRIME	NA
contig00141	339	1000	CATA	0/0	98.7	100.0	MEG_1593	Drugs:Phenicol:Chloramphenicol_acetyltransferases:CATA	NA
contig00052	12748	13623	CMY	0/0	100.0	94.1	MEG_1992	Drugs:betalactams:Class_C_betalactamases:CMY	NA
contig00052	13755	14982	CMY	0/0	100.0	99.6	MEG_1958	Drugs:betalactams:Class_C_betalactamases:CMY	NA
contig00051	1023	1965	CTX	0/0	100.0	97.2	MEG_2435	Drugs:betalactams:Class_A_betalactamases:CTX	NA
contig00082	2855	3352	DFRA	0/0	100.0	100.0	MEG_2551	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00137	442	915	DFRA	0/0	100.0	99.8	MEG_2517	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00014	49710	50123	HNS	0/0	100.0	90.3	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00139	69	990	MPHA	1/1	100.0	99.7	MEG_4030	Drugs:MLS:Macrolide_phosphotransferases:MPHA	NA
contig00113	577	1407	OXA	0/0	100.0	100.0	MEG_4980	Drugs:betalactams:Class_D_betalactamases:OXA	NA
contig00109	60	392	QACF	0/0	100.0	100.0	MEG_5838	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:QACF	NA
contig00075	4364	5045	QNRB	1/1	100.0	99.1	MEG_5928	Drugs:Fluoroquinolones:Quinolone_resistance_protein_Qnr:QNRB	NA
contig00082	185	1152	SULI	0/0	100.0	100.0	MEG_6615	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULI	NA
contig00083	2980	3795	SULII	0/0	100.0	100.0	MEG_6617	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULII	NA
contig00088	1524	2723	TETA	0/0	100.0	100.0	MEG_7021	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETA	NA
contig00093	1638	2822	TETC	0/0	100.0	99.9	MEG_7061	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETC	NA

ORTHO08HW

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00070	1693	2553	aac(3)-IIa_1	0/0	100	99.8	X51534	aac(3)-IIa	Gentamicin, Tobramycin
contig00072	1539	2138	aac(6’)-Ib-cr_1	0/0	100	100.0	DQ303918	aac(6’)-Ib-cr	Ciprofloxacin
contig00066	843	1646	aph(3’’)-Ib_5	0/0	100	100.0	AF321551	aph(3’’)-Ib	Streptomycin
contig00080	134	949	aph(3’)-Ia_1	0/0	100	100.0	V00359	aph(3’)-Ia
contig00066	7	843	aph(6)-Id_1	0/0	100	100.0	M28829	aph(6)-Id	Streptomycin
contig00028	2635	3510	blaCTX-M-15_1	0/0	100	100.0	AY044436	blaCTX-M-15	Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig00072	578	1408	blaOXA-1_1	0/0	100	100.0	HQ170510	blaOXA-1	Amoxicillin, Amoxicillin+Clavulanic_acid, Ampicillin, Ampicillin+Clavulanic_acid, Cefepime, Piperacillin, Piperacillin+Tazobactam
contig00074	533	1393	blaTEM-1B_1	0/0	100	100.0	AY458016	blaTEM-1B	Amoxicillin, Ampicillin, Cephalothin, Piperacillin, Ticarcillin
contig00056	9663	10322	catA1_1	0/0	100	99.8	V00622	catA1	Chloramphenicol
contig00056	3168	3650	dfrA14_5	0/0	100	99.6	DQ388123	dfrA14	Trimethoprim
contig00029	3070	4302	mdf(A)_1	0/0	100	98.8	Y08743	mdf(A)
contig00079	69	990	mph(A)_2	1/1	100	99.7	U36578	mph(A)	Erythromycin, Azithromycin, Spiramycin, Telithromycin
contig00066	1707	2522	sul2_3	0/0	100	100.0	HQ840942	sul2	Sulfamethoxazole
contig00065	2274	3479	tet(B)_2	0/0	100	100.0	AF326777	tet(B)	Doxycycline, Tetracycline, Minocycline

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00070	1693	2553	AAC(3)-IIe	0/0	100.0	99.5	EU022315.1:0-861	AAC(3)-IIe is a plasmid-encoded aminoglycoside acetyltransferase in E. coli	aminoglycoside
contig00072	1539	2138	AAC(6’)-Ib-cr	0/0	100.0	100.0	DQ303918:0-600	AAC(6’)-Ib-cr is an aminoglycoside acetyltransferase encoded by plasmids transposons integrons in Enterobacteriaceae. The aac(6’)-Ib-cr variant gene can induce resistance against aminoglycoside and fluoroquinolone simultaneously	aminoglycoside, fluoroquinolone
contig00005	89400	92549	acrB	0/0	100.0	99.1	U00096.3:484403-481253	Protein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug/proton antiporter.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00002	219346	222459	acrD	0/0	100.0	99.0	AP009048.1:2586250-2589364	AcrD is an aminoglycoside efflux pump expressed in E. coli. Its expression can be induced by indole and is regulated by baeRS and cpxAR.	aminoglycoside
contig00012	117960	119117	acrE	0/0	100.0	99.0	U00096:3413863-3415021	AcrE is a membrane fusion protein similar to AcrA.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00012	119129	122233	acrF	0/0	100.0	99.1	U00096:3415032-3418137	AcrF is a inner membrane transporter similar to AcrB.	cephalosporin, cephamycin, fluoroquinolone, penam
contig00012	116899	117561	acrS	0/0	100.0	99.4	U00096:3413465-3412802	AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.	cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00066	843	1646	APH(3’’)-Ib	0/0	100.0	99.8	AF313472:15593-16397	APH(3’’)-Ib is an aminoglycoside phosphotransferase encoded by plasmids transposons integrative conjugative elements and chromosomes in Enterobacteriaceae and Pseudomonas spp.	aminoglycoside
contig00080	136	949	APH(3’)-Ia	0/0	99.8	99.4	BX664015.1:103833-103017	APH(3’)-Ia is a transposon-encoded aminoglycoside phosphotransferase in E. coli and S. enterica. It is identical at the protein sequence to APH(3’)-Ic an aminoglycoside phosphotransferase encoded by plasmids transposons and genomic islands in K. pneumoniae A. baumannii S. marcescens Corynebacterium spp. Photobacterium spp. and Citrobacter spp.	aminoglycoside
contig00066	7	843	APH(6)-Id	0/0	100.0	99.9	AF024602:3155-3992	APH(6)-Id is an aminoglycoside phosphotransferase encoded by plasmids integrative conjugative elements and chromosomal genomic islands in K. pneumoniae Salmonella spp. E. coli Shigella flexneri Providencia alcalifaciens Pseudomonas spp. V. cholerae Edwardsiella tarda Pasteurella multocida and Aeromonas bestiarum	aminoglycoside
contig00024	70234	71055	bacA	0/0	100.0	98.7	U00096.3:3204131-3203309	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
contig00004	104834	105556	baeR	0/0	100.0	99.5	AP009048.1:2166412-2167135	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	aminocoumarin, aminoglycoside
contig00004	103434	104837	baeS	0/0	100.0	98.0	AP009048:2165012-2166416	BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.	aminocoumarin, aminoglycoside
contig00056	9663	10322	catI	0/0	100.0	99.8	V00622:243-903	catI is a chromosome and transposon-encoded variant of the cat gene found in Escherichia coli and Acinetobacter baumannii	phenicol
contig00022	22831	24204	cpxA	0/0	100.0	98.6	BA000007.3:4905062-4903688	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	aminocoumarin, aminoglycoside
contig00006	14925	15557	CRP	0/0	100.0	99.2	AP009048.1:4154296-4153663	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	fluoroquinolone, macrolide, penam
contig00028	2635	3510	CTX-M-15	0/0	100.0	100.0	AY044436:1435-2311	CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family	cephalosporin
contig00056	3168	3650	dfrA14	0/0	100.0	99.8	EU780012:2162-2645	dfrA14 is an integron-encoded dihydrofolate reductase found in Escherichia coli	diaminopyrimidine
contig00039	5182	6354	emrA	0/0	100.0	97.5	AP009048:2810082-2811255	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	fluoroquinolone
contig00039	3627	5165	emrB	0/0	100.0	99.9	U00096:2812615-2814154	emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin.	fluoroquinolone
contig00002	123600	124655	emrK	0/0	100.0	99.7	D78168:536-1592	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	tetracycline
contig00039	6481	7011	emrR	0/0	100.0	100.0	U00096.3:2810769-2811300	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	fluoroquinolone
contig00002	122056	123600	emrY	1/6	100.0	99.3	D78168:1591-3130	emrY is a multidrug transport that moves substrates across the inner membrane of the Gram-negative E. coli. It is a homolog of emrB.	tetracycline
contig00016	88523	90166	eptA	0/0	100.0	99.3	AP009048:4340268-4338624	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
contig00005	92572	93765	Escherichia_coli_acrA	0/0	100.0	99.8	U00096.3:485619-484425	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00010	139347	140480	Escherichia_coli_ampC	0/0	100.0	97.3	U00096.3:4378944-4377810	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin, penam
contig00002	186924	188228	Escherichia_coli_ampC1_beta-lactamase	0/0	100.0	98.6	FN649414.1:2765050-2766355	An ampC-like beta-lactamase identified from Escherichia coli.	cephalosporin, penam
contig00005	3380	4537	Escherichia_coli_ampH	0/0	100.0	99.4	AP012030.1:396711-395553	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin, penam
contig00011	2794	3126	Escherichia_coli_emrE	0/0	100.0	91.9	Z11877.1:485-818	Member of the small MDR (multidrug resistance) family of transporters, in Escherichia coli this protein provides resistance against a number of positively charged compounds including ethidium bromide and erythromycin, proton-dependent secondary transporter which exchanges protons for compound translocation	macrolide
contig00029	3070	4302	Escherichia_coli_mdfA	0/0	100.0	97.2	JQ394987:0-1233	Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter.	benzalkonium_chloride, rhodamine, tetracycline
contig00002	125179	125793	evgA	0/0	100.0	99.0	BA000007.3:3212025-3212640	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	fluoroquinolone, macrolide, penam, tetracycline
contig00002	125798	129391	evgS	0/0	100.0	99.4	U00096:2484373-2487967	EvgS is a sensor protein that phosphorylates the regulatory protein EvgA. evgS corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	fluoroquinolone, macrolide, penam, tetracycline
contig00040	2699	3427	gadW	0/0	100.0	94.4	CP015085.1:2552440-2551711	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	fluoroquinolone, macrolide, penam
contig00040	1507	2331	gadX	0/0	100.0	97.9	AP009048.1:3974604-3975429	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	fluoroquinolone, macrolide, penam
contig00007	173074	173487	H-NS	0/0	100.0	99.5	BA000007.3:1738104-1737690	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00020	8282	8954	kdpE	0/0	99.3	97.2	U00096.3:721733-721055	kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding.	aminoglycoside
contig00001	390275	390658	marA	0/0	100.0	99.5	AP009048.1:1621287-1621671	In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.	carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00004	94574	95821	mdtA	0/0	100.0	98.2	U00096:2154015-2155263	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	aminocoumarin
contig00004	95821	98943	mdtB	0/0	100.0	99.8	U00096:2155262-2158385	MdtB is a transporter that forms a heteromultimer complex with MdtC to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex.	aminocoumarin
contig00004	98944	102021	mdtC	0/0	100.0	98.6	U00096:2158385-2161463	MdtC is a transporter that forms a heteromultimer complex with MdtB to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex. In the absence of MdtB MdtC can form a homomultimer complex that results in a functioning efflux complex with a narrower drug specificity. mdtC corresponds to 3 loci in Pseudomonas aeruginosa PAO1 (gene name: muxC/muxB) and 3 loci in Pseudomonas aeruginosa LESB58.	aminocoumarin
contig00040	6928	8085	mdtE	0/0	100.0	99.7	AP009048.1:3981183-3980025	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	fluoroquinolone, macrolide, penam
contig00040	3790	6903	mdtF	0/0	100.0	98.5	U00096:3660413-3663527	MdtF is the multidrug inner membrane transporter for the MdtEF-TolC efflux complex.	fluoroquinolone, macrolide, penam
contig00017	86688	87914	mdtG	0/0	100.0	99.3	CP000800.1:1192954-1191727	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	fosfomycin
contig00017	76849	78057	mdtH	0/0	100.0	98.4	U00096:1125326-1124117	Multidrug resistance protein MdtH	fluoroquinolone
contig00003	220474	221706	mdtM	0/0	100.0	96.3	U00096.3:4568519-4567286	Multidrug resistance protein MdtM	acridine_dye, fluoroquinolone, lincosamide, nucleoside, phenicol
contig00038	26562	27593	mdtN	0/0	100.0	98.1	AP009048.1:4307588-4306556	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	acridine_dye, nucleoside
contig00038	24511	26562	mdtO	0/0	100.0	98.4	AP009048.1:4306557-4304505	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00038	23048	24514	mdtP	0/0	100.0	98.2	AP009048.1:4304509-4303042	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	acridine_dye, nucleoside
contig00079	69	974	mphA	0/0	100.0	100.0	D16251.1:2531-1625	The mphA gene encodes for resistance enzyme MPH(2’)-I which preferentially inactivate 14-membered macrolides (e.g.erythromycin telithromycin roxithromycin) over 16-membered macrolides (e.g.tylosin spiramycin). It phosphorylates macrolides at 2’-OH hydroxyl of desosamine sugar of macrolides in a GTP-dependent manner.	macrolide
contig00002	243696	244170	mphB	0/0	99.6	97.5	AE005174.2:3397370-3397847	The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides.	macrolide
contig00008	51499	53247	msbA	0/0	100.0	99.4	U00096.3:966620-968369	MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability.	nitroimidazole
contig00072	578	1408	OXA-1	0/0	100.0	100.0	JN420336.1:2230-1399	OXA-1 is a beta-lactamase found in E. coli	cephalosporin, penam
contig00002	17921	18889	pmrF	0/0	100.0	99.3	U00096:2367070-2368039	PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	peptide
contig00066	1707	2522	sul2	0/0	100.0	99.6	AY055428.1:21084-20268	Sul2 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria usually found on small plasmids.	sulfonamide
contig00074	533	1393	TEM-1	0/0	100.0	99.9	AL513383:161910-162771	TEM-1 is a broad-spectrum beta-lactamase found in many Gram-negative bacteria. Confers resistance to penicillins and first generation cephalosphorins.	cephalosporin, monobactam, penam, penem
contig00065	2274	3479	tet(B)	0/0	100.0	99.8	AB089595:0-1206	Tet(B) is a tetracycline efflux protein expressed in many Gram-negative bacteria. It confers resistance to tetracycline doxycycline and minocycline but not tigecycline.	tetracycline
contig00023	73061	74548	tolC	0/0	100.0	99.7	FJ768952:0-1488	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan
contig00033	42513	44156	yojI	0/0	100.0	98.1	U00096.3:2308615-2306971	YojI mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. YojI is capable of pumping out microcin molecules. The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI.	peptide

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00070	1693	2553	(AGly)aac3-IIa	0/0	100	99.8	X51534:91-951	(AGly)aac3-IIa	NA
contig00080	134	949	(AGly)aph3-Ia	0/0	100	99.9	HQ840942:23569-24384	(AGly)aph3-Ia	NA
contig00066	843	1646	(AGly)strA	0/0	100	99.9	AB366441:22458-23261	(AGly)strA	NA
contig00066	7	843	(AGly)strB	0/0	100	100.0	FJ474091:264-1100	(AGly)strB	NA
contig00002	186924	188228	(Bla)AmpC1_Ecoli	0/0	100	98.6	FN649414:2765051-2766355	(Bla)AmpC1_Ecoli	NA
contig00010	139347	140480	(Bla)AmpC2_Ecoli	0/0	100	97.3	CP002970:332756-333889	(Bla)AmpC2_Ecoli	NA
contig00005	3380	4537	(Bla)ampH_Ecoli	0/0	100	99.4	AP012030:395554-396711	(Bla)ampH_Ecoli	NA
contig00028	2635	3510	(Bla)blaCTX-M-15	0/0	100	100.0	JQ686199:261-1136	(Bla)blaCTX-M-15	NA
contig00072	578	1408	(Bla)blaOXA-1	0/0	100	100.0	JQ682867:1-831	(Bla)blaOXA-1	NA
contig00074	533	1393	(Bla)blaTEM-105	0/0	100	99.9	AF516720:215-1075	(Bla)blaTEM-105	NA
contig00020	61082	62983	(Bla)Penicillin_Binding_Protein_Ecoli	0/0	100	99.0	CP002291:664439-666340	(Bla)Penicillin_Binding_Protein_Ecoli	NA
contig00079	69	974	(MLS)mph(A)	0/0	100	100.0	DQ445270:1626-2531	(MLS)mph(A)	NA
contig00056	9663	10322	(Phe)catA1	0/0	100	99.8	V00622:244-903	(Phe)catA1	NA
contig00066	1707	2522	(Sul)sul2	0/0	100	99.6	EU360945:1617-2432	(Sul)sul2	NA
contig00065	2274	3479	(Tet)tetB	0/0	100	99.7	AB089594:1-1206	(Tet)tetB	NA
contig00056	3168	3641	(Tmt)dfrA14	0/0	100	100.0	GU726917:72-545	(Tmt)dfrA14	NA

NCBI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00070	1693	2553	aac(3)-IIe	0/0	100	99.8	NG_047244.1	aminoglycoside N-acetyltransferase AAC(3)-IIe	GENTAMICIN
contig00072	1539	2093	aac(6’)-Ib-D181Y	0/0	100	99.8	NG_067946.1	AAC(6’)-Ib family aminoglycoside 6’-N-acetyltransferase	AMIKACIN, KANAMYCIN, TOBRAMYCIN
contig00066	843	1670	aph(3’’)-Ib	0/0	100	100.0	NG_056002.2	aminoglycoside O-phosphotransferase APH(3’’)-Ib	STREPTOMYCIN
contig00080	134	949	aph(3’)-Ia	0/0	100	100.0	NG_047430.1	aminoglycoside O-phosphotransferase APH(3’)-Ia	KANAMYCIN
contig00066	7	843	aph(6)-Id	0/0	100	100.0	NG_047464.1	aminoglycoside O-phosphotransferase APH(6)-Id	STREPTOMYCIN
contig00028	2635	3510	blaCTX-M-15	0/0	100	100.0	NG_048935.1	class A extended-spectrum beta-lactamase CTX-M-15	CEPHALOSPORIN
contig00010	139347	140480	blaEC-15	0/0	100	98.6	NG_049081.1	class C extended-spectrum beta-lactamase EC-15	CEPHALOSPORIN
contig00072	578	1408	blaOXA-1	0/0	100	100.0	NG_049392.1	oxacillin-hydrolyzing class D beta-lactamase OXA-1	CEPHALOSPORIN
contig00074	533	1393	blaTEM-1	0/0	100	100.0	NG_050145.1	class A broad-spectrum beta-lactamase TEM-1	BETA-LACTAM
contig00056	9663	10322	catA1	0/0	100	99.8	NG_047582.1	type A-1 chloramphenicol O-acetyltransferase	CHLORAMPHENICOL
contig00056	3168	3641	dfrA14	0/0	100	100.0	NG_056035.1	trimethoprim-resistant dihydrofolate reductase DfrA14	TRIMETHOPRIM
contig00079	69	990	mph(A)	1/1	100	99.7	NG_047986.1	Mph(A) family macrolide 2’-phosphotransferase	MACROLIDE
contig00066	1707	2522	sul2	0/0	100	99.9	NG_048118.1	sulfonamide-resistant dihydropteroate synthase Sul2	SULFONAMIDE
contig00065	2274	3479	tet(B)	0/0	100	100.0	NG_048163.1	tetracycline efflux MFS transporter Tet(B)	TETRACYCLINE

MEGARES

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
contig00070	1693	2553	AAC3	0/0	100.0	99.8	MEG_44	Drugs:Aminoglycosides:Aminoglycoside_N-acetyltransferases:AAC3	NA
contig00005	92572	93765	ACRA	0/0	100.0	99.8	MEG_399	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA	NA
contig00005	89400	92549	ACRB	0/0	100.0	99.1	MEG_401	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRB	NA
contig00002	219346	222459	ACRD	0/0	100.0	99.0	MEG_407	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ACRD	NA
contig00012	117960	119117	ACRE	0/0	100.0	99.0	MEG_408	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRE	NA
contig00012	119129	122233	ACRF	0/0	100.0	99.1	MEG_409	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRF	NA
contig00012	116899	117561	ACRS	0/0	100.0	99.4	MEG_415	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS	NA
contig00005	3380	4537	AMPH	0/0	100.0	99.4	MEG_729	Drugs:betalactams:Penicillin_binding_protein:AMPH	NA
contig00066	843	1670	APH3-DPRIME	0/0	100.0	100.0	MEG_1019	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH3-DPRIME	NA
contig00080	134	949	APH3-PRIME	0/0	100.0	100.0	MEG_1079	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH3-PRIME	NA
contig00066	7	843	APH6	0/0	100.0	100.0	MEG_1086	Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH6	NA
contig00004	80054	81906	ASMA	0/0	100.0	98.0	MEG_1180	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:ASMA	NA
contig00024	70234	71055	BACA	0/0	100.0	98.9	MEG_1189	Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA	NA
contig00004	104834	105556	BAER	0/0	100.0	99.5	MEG_1192	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER	NA
contig00004	103434	104837	BAES	0/0	100.0	98.0	MEG_1193	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES	NA
contig00004	218030	219220	BCR	0/0	100.0	96.6	MEG_1210	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR	NA
contig00010	139347	140480	BLAEC	0/0	100.0	98.6	MEG_1282	Drugs:betalactams:Class_C_betalactamases:BLAEC	NA
contig00056	9663	10333	CATA	0/0	100.0	100.0	MEG_1593	Drugs:Phenicol:Chloramphenicol_acetyltransferases:CATA	NA
contig00022	22136	22834	CPXAR	0/0	100.0	99.1	MEG_2118	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00022	22831	24204	CPXAR	0/0	100.0	99.2	MEG_2121	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR	NA
contig00006	14925	15557	CRP	0/0	100.0	99.2	MEG_2132	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP	NA
contig00056	3168	3641	DFRA	0/0	100.0	99.8	MEG_2517	Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA	NA
contig00039	5182	6354	EMRA	0/0	100.0	97.5	MEG_2722	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA	NA
contig00039	3627	5165	EMRB	0/0	100.0	99.9	MEG_2725	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRB	NA
contig00014	22120	23310	EMRD	0/0	100.0	99.9	MEG_2729	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD	NA
contig00002	123600	124763	EMRK	0/0	100.0	99.7	MEG_2732	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK	NA
contig00039	6481	7011	EMRR	0/0	100.0	100.0	MEG_2734	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR	NA
contig00002	122056	123600	EMRY	1/6	100.0	99.3	MEG_2736	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRY	NA
contig00016	88523	90166	EPTA	0/0	100.0	99.3	MEG_2739	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA	NA
contig00002	125798	129391	EVGS	0/0	100.0	99.4	MEG_2870	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EVGS	NA
contig00040	2699	3427	GADW	0/0	100.0	98.6	MEG_3081	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW	NA
contig00040	1507	2331	GADX	0/0	100.0	97.9	MEG_3083	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX	NA
contig00007	173074	173487	HNS	0/0	100.0	99.5	MEG_3271	Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS	NA
contig00020	8282	8954	KDPE	0/0	99.3	97.2	MEG_3448	Drugs:Aminoglycosides:Aminoglycoside_efflux_pumps:KDPE	NA
contig00001	390275	390664	MARA	0/0	100.0	99.5	MEG_3662	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA	NA
contig00001	390678	391112	MARR	0/0	100.0	98.2	MEG_3663	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR	NA
contig00029	3070	4302	MDFA	0/0	100.0	98.9	MEG_3737	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDFA	NA
contig00004	94574	95821	MDTA	0/0	100.0	98.2	MEG_3746	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA	NA
contig00004	95821	98943	MDTB	0/0	100.0	99.8	MEG_3747	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTB	NA
contig00004	98944	102021	MDTC	0/0	100.0	98.6	MEG_3749	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTC	NA
contig00040	6928	8085	MDTE	0/0	100.0	99.7	MEG_3751	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE	NA
contig00040	3790	6903	MDTF	0/0	100.0	98.5	MEG_3752	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTF	NA
contig00017	86688	87914	MDTG	0/0	100.0	99.5	MEG_3753	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG	NA
contig00017	76849	78057	MDTH	0/0	100.0	98.4	MEG_3755	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTH	NA
contig00001	328706	329035	MDTI	0/0	100.0	99.4	MEG_3756	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI	NA
contig00001	328354	328719	MDTJ	0/0	100.0	99.5	MEG_3757	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ	NA
contig00001	257347	258720	MDTK	0/0	100.0	99.0	MEG_3759	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:MDTK	NA
contig00003	220474	221706	MDTM	0/0	100.0	96.3	MEG_3761	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTM	NA
contig00038	26562	27593	MDTN	0/0	100.0	98.1	MEG_3763	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN	NA
contig00038	24511	26562	MDTO	0/0	100.0	98.4	MEG_3764	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTO	NA
contig00038	23048	24514	MDTP	0/0	100.0	98.2	MEG_3765	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP	NA
contig00079	69	990	MPHA	1/1	100.0	99.7	MEG_4030	Drugs:MLS:Macrolide_phosphotransferases:MPHA	NA
contig00002	243696	244170	MPHB	0/0	99.6	97.5	MEG_4033	Drugs:MLS:Macrolide_phosphotransferases:MPHB	NA
contig00008	51499	53247	MSBA	0/0	100.0	99.4	MEG_4061	Drugs:Multi-drug_resistance:Multi-drug_ABC_efflux_pumps:MSBA	NA
contig00011	2794	3126	MVRC	0/0	100.0	91.9	MEG_4103	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MVRC	NA
contig00072	578	1408	OXA	0/0	100.0	100.0	MEG_4980	Drugs:betalactams:Class_D_betalactamases:OXA	NA
contig00020	61082	62983	PBP2	0/0	100.0	99.0	MEG_5400	Drugs:betalactams:Penicillin_binding_protein:PBP2	NA
contig00002	186924	188228	PBP4B	0/0	100.0	98.6	MEG_5409	Drugs:betalactams:Penicillin_binding_protein:PBP4B	NA
contig00002	17921	18889	PMRF	0/0	100.0	99.3	MEG_5801	Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF	NA
contig00003	156554	157423	ROBA	0/0	100.0	99.0	MEG_6082	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA	NA
contig00038	1110	1432	SOXS	0/0	99.7	99.7	MEG_6551	Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS	NA
contig00066	1707	2522	SULII	0/0	100.0	100.0	MEG_6618	Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULII	NA
contig00074	515	1760	TEM	0/0	98.3	99.2	MEG_6875	Drugs:betalactams:Class_A_betalactamases:TEM	NA
contig00065	2274	3479	TETB	0/0	100.0	100.0	MEG_7052	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETB	NA
contig00065	4273	4689	TETD	0/0	100.0	100.0	MEG_7070	Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETD	NA
contig00033	42513	44156	YOGI	0/0	100.0	98.1	MEG_7842	Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:YOGI	NA

Summary figures

Presence/Absence of antibiotic resistance genes (coverage and identity > 90%) on each sample

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Plasmid Profiling

Field	Description
Contig	Contig name where the gene was found
Start	Start position of the gene within the contig
End	End position of the gene within the contig
Gene	Antibiotic resistance gene
Gaps	Gaps in subject (genome) and query (antibiotic resistance gene)
Coverage	Proportion (%) of the gene covered
Identity	Proportion (%) of exact nucleotide matches
Accession	Accesion number of the antibiotic resistance gene
Product	Antibiotic resistance gene product

Select sample

ID002

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00103	1011	1120	Col440I_1	0/0	96.5	91.8	CP023920.1	Col440I_1__CP023920.1
contig00133	155	268	Col440I_1	0/0	100.0	96.5	CP023920.1	Col440I_1__CP023920.1
contig00132	1049	1608	IncFIB(pECLA)_1_pECLA	0/0	100.0	100.0	CP001919	IncFIB(pECLA)_1_pECLA_CP001919

ID003

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00058	2468	2598	ColRNAI_1	1/1	100	90.1	DQ298019	ColRNAI_1__DQ298019
contig00049	3863	4627	IncY_1	0/0	100	98.8	K02380	IncY_1__K02380

ID005

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00112	400	632	Col(BS512)_1	0/0	100	100.0	NC_010656	Col(BS512)_1__NC_010656
contig00096	3274	3427	Col156_1	0/0	100	94.8	NC_009781	Col156_1__NC_009781
contig00039	15730	16372	IncFIB(pB171)_1_pB171	0/0	100	99.4	AB024946	IncFIB(pB171)_1_pB171_AB024946
contig00055	16887	17147	IncFII(pRSB107)_1_pRSB107	0/0	100	100.0	AJ851089	IncFII(pRSB107)_1_pRSB107_AJ851089
contig00033	24651	25415	IncY_1	0/0	100	99.7	K02380	IncY_1__K02380

ID006

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00098	226	739	IncN_1	0/0	100	100.0	AY046276	IncN_1__AY046276
contig00089	4434	5198	IncY_1	0/0	100	99.1	K02380	IncY_1__K02380

ID007I

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00134	429	690	Col(MG828)_1	0/0	100.0	92.0	NC_008486	Col(MG828)_1__NC_008486
contig00070	378	519	Col156_1	0/0	92.2	98.6	NC_009781	Col156_1__NC_009781
contig00093	2967	3120	Col156_1	0/0	100.0	94.8	NC_009781	Col156_1__NC_009781
contig00079	3365	3752	IncFIA_1	0/0	100.0	100.0	AP001918	IncFIA_1__AP001918
contig00073	8473	9154	IncFIB(AP001918)_1	0/0	100.0	98.0	AP001918	IncFIB(AP001918)_1__AP001918
contig00108	1556	1815	IncFII(pCoo)_1_pCoo	2/4	98.8	95.1	CR942285	IncFII(pCoo)_1_pCoo_CR942285
contig00094	1135	1395	IncFII(pRSB107)_1_pRSB107	0/0	100.0	100.0	AJ851089	IncFII(pRSB107)_1_pRSB107_AJ851089
contig00054	7790	7931	IncI1_1_Alpha	0/0	100.0	98.6	AP005147	IncI1_1_Alpha_AP005147

ID011

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00068	400	632	Col(BS512)_1	0/0	100.0	100.0	NC_010656	Col(BS512)_1__NC_010656
contig00047	2894	3035	Col156_1	0/0	92.2	98.6	NC_009781	Col156_1__NC_009781
contig00053	3338	3491	Col156_1	0/0	100.0	94.8	NC_009781	Col156_1__NC_009781
contig00034	19761	20148	IncFIA_1	0/0	100.0	99.7	AP001918	IncFIA_1__AP001918
contig00034	8473	9154	IncFIB(AP001918)_1	0/0	100.0	99.7	AP001918	IncFIB(AP001918)_1__AP001918

ID013I

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00056	2962	3103	Col156_1	0/0	92.2	98.6	NC_009781	Col156_1__NC_009781
contig00043	19761	20148	IncFIA_1	0/0	100.0	99.7	AP001918	IncFIA_1__AP001918
contig00043	8473	9154	IncFIB(AP001918)_1	0/0	100.0	99.7	AP001918	IncFIB(AP001918)_1__AP001918
contig00076	255	515	IncFII(pRSB107)_1_pRSB107	0/0	100.0	100.0	AJ851089	IncFII(pRSB107)_1_pRSB107_AJ851089
contig00022	65094	65978	p0111_1	0/0	100.0	98.9	AP010962	p0111_1__AP010962

ID016I

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00364	2465	2578	Col440I_1	0/0	100	96.5	CP023920.1	Col440I_1__CP023920.1
contig00433	646	759	Col440I_1	0/0	100	91.2	CP023920.1	Col440I_1__CP023920.1
contig00180	7748	8135	IncFIA_1	0/0	100	99.7	AP001918	IncFIA_1__AP001918
contig00288	4186	4867	IncFIB(AP001918)_1	0/0	100	98.4	AP001918	IncFIB(AP001918)_1__AP001918
contig00375	1143	1562	IncHI1A(CIT)_1_pNDM-CIT	0/0	100	100.0	JX182975	IncHI1A(CIT)_1_pNDM-CIT_JX182975
contig00147	8324	8861	IncHI1B(CIT)_1_pNDM-CIT	0/0	100	100.0	JX182975	IncHI1B(CIT)_1_pNDM-CIT_JX182975
contig00039	41798	42373	IncX5_2	0/0	100	100.0	MF062700.1	IncX5_2__MF062700.1

ID017

## [1] "NO PLASMID FOUND!!"

ID018CT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00105	2794	3475	IncFIB(AP001918)_1	0/0	100	98.4	AP001918	IncFIB(AP001918)_1__AP001918
contig00079	13392	14136	IncP1_3	0/0	100	100.0	KX377410	IncP1_3__KX377410
contig00083	2157	3041	p0111_1	0/0	100	98.6	AP010962	p0111_1__AP010962

ID019

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00058	336	449	Col440I_1	0/0	100	93.9	CP023920.1	Col440I_1__CP023920.1

ID01CT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00082	519	632	Col440I_1	0/0	100	90.3	CP023920.1	Col440I_1__CP023920.1
contig00013	81165	81491	IncHI2_1	0/0	100	100.0	BX664015	IncHI2_1__BX664015
contig00013	96357	96986	IncHI2A_1	0/0	100	100.0	BX664015	IncHI2A_1__BX664015

ID021

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00047	3388	3775	IncFIA_1	0/0	100	99.7	AP001918	IncFIA_1__AP001918
contig00047	19923	20604	IncFIB(AP001918)_1	0/0	100	98.4	AP001918	IncFIB(AP001918)_1__AP001918

ID027

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00062	346	499	Col156_1	0/0	100	98.7	NC_009781	Col156_1__NC_009781
contig00049	9099	9482	IncFIA_1	0/0	99	99.7	AP001918	IncFIA_1__AP001918
contig00053	9046	9727	IncFIB(AP001918)_1	0/0	100	98.4	AP001918	IncFIB(AP001918)_1__AP001918

ID031

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00143	400	632	Col(BS512)_1	0/0	100	100.0	NC_010656	Col(BS512)_1__NC_010656
contig00148	433	694	Col(MG828)_1	0/0	100	92.8	NC_008486	Col(MG828)_1__NC_008486
contig00116	4077	4230	Col156_1	0/0	100	94.8	NC_009781	Col156_1__NC_009781
contig00069	1832	2513	IncFIB(AP001918)_1	0/0	100	98.4	AP001918	IncFIB(AP001918)_1__AP001918
contig00082	2741	3505	IncY_1	0/0	100	99.0	K02380	IncY_1__K02380

ID034I

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00059	3095	3776	IncFIB(AP001918)_1	0/0	100	98.4	AP001918	IncFIB(AP001918)_1__AP001918

ID041

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00040	24148	24650	IncFIC(FII)_1	2/4	100	95.6	AP001918	IncFIC(FII)_1__AP001918
contig00061	3030	3794	IncY_1	0/0	100	98.8	K02380	IncY_1__K02380

ID043I

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00066	9109	9492	IncFIA_1	0/0	99	99.7	AP001918	IncFIA_1__AP001918
contig00091	1834	2515	IncFIB(AP001918)_1	0/0	100	98.4	AP001918	IncFIB(AP001918)_1__AP001918

ID044

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00137	400	632	Col(BS512)_1	0/0	100.0	100.0	NC_010656	Col(BS512)_1__NC_010656
contig00069	9239	9626	IncFIA_1	0/0	100.0	99.7	AP001918	IncFIA_1__AP001918
contig00098	7051	7732	IncFIB(AP001918)_1	0/0	100.0	98.4	AP001918	IncFIB(AP001918)_1__AP001918
contig00122	3602	3838	IncFII(pAMA1167-NDM-5)_1_pAMA1167-NDM-5	0/0	90.8	97.5	CP024805.1	IncFII(pAMA1167-NDM-5)_1_pAMA1167-NDM-5_CP024805.1

ID046II

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00362	2792	2901	Col440I_1	0/0	96.5	96.4	CP023920.1	Col440I_1__CP023920.1
contig00063	735	1294	IncFIB(K)_1_Kpn3	0/0	100.0	98.9	JN233704	IncFIB(K)_1_Kpn3_JN233704
contig00022	3494	4031	IncHI1B(CIT)_1_pNDM-CIT	0/0	100.0	93.5	JX182975	IncHI1B(CIT)_1_pNDM-CIT_JX182975
contig00001	38199	38963	IncY_1	0/0	100.0	98.8	K02380	IncY_1__K02380
contig00004	23923	24917	pSL483_1	0/0	100.0	93.0	CP001137	pSL483_1__CP001137

ID049

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00104	6252	6639	IncFIA_1	0/0	100	99.5	AP001918	IncFIA_1__AP001918
contig00077	1832	2513	IncFIB(AP001918)_1	0/0	100	97.2	AP001918	IncFIB(AP001918)_1__AP001918
contig00068	19181	19441	IncFII(pRSB107)_1_pRSB107	0/0	100	99.6	AJ851089	IncFII(pRSB107)_1_pRSB107_AJ851089

ID051

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00047	3584	3725	Col156_1	0/0	92.2	98.6	NC_009781	Col156_1__NC_009781
contig00054	3142	3295	Col156_1	0/0	100.0	94.8	NC_009781	Col156_1__NC_009781
contig00034	19761	20148	IncFIA_1	0/0	100.0	99.7	AP001918	IncFIA_1__AP001918
contig00034	8473	9154	IncFIB(AP001918)_1	0/0	100.0	99.7	AP001918	IncFIB(AP001918)_1__AP001918

ID054

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00043	5286	6050	IncY_1	0/0	100	98.8	K02380	IncY_1__K02380

ID057

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00062	2909	3062	Col156_1	0/0	100	98.7	NC_009781	Col156_1__NC_009781
contig00052	9119	9502	IncFIA_1	0/0	99	99.7	AP001918	IncFIA_1__AP001918
contig00059	8470	9151	IncFIB(AP001918)_1	0/0	100	98.4	AP001918	IncFIB(AP001918)_1__AP001918

ID066II

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig01182	400	632	Col(BS512)_1	0/0	100.0	100.0	NC_010656	Col(BS512)_1__NC_010656
contig00131	3630	3771	Col156_1	0/0	92.2	98.6	NC_009781	Col156_1__NC_009781
contig00235	5514	5644	ColRNAI_1	1/1	100.0	90.1	DQ298019	ColRNAI_1__DQ298019
contig00613	2056	2737	IncFIB(AP001918)_1	0/0	100.0	98.0	AP001918	IncFIB(AP001918)_1__AP001918

ID067

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00041	23923	24917	pSL483_1	0/0	100	93	CP001137	pSL483_1__CP001137

ID068

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00059	2189	2870	IncFIB(AP001918)_1	0/0	100	96.8	AP001918	IncFIB(AP001918)_1__AP001918
contig00039	4843	5402	IncFIB(K)_1_Kpn3	0/0	100	98.9	JN233704	IncFIB(K)_1_Kpn3_JN233704

ID073I

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00061	2382	3063	IncFIB(AP001918)_1	0/0	100	96.9	AP001918	IncFIB(AP001918)_1__AP001918
contig00073	3423	3982	IncFIB(K)_1_Kpn3	0/0	100	98.9	JN233704	IncFIB(K)_1_Kpn3_JN233704

ID077

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00048	3030	3794	IncY_1	0/0	100	98.8	K02380	IncY_1__K02380

ID081I

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00138	1071	1332	Col(MG828)_1	0/0	100.0	93.1	NC_008486	Col(MG828)_1__NC_008486
contig00040	5825	5979	IncB/O/K/Z_2	1/1	96.2	96.1	GU256641	IncB/O/K/Z_2__GU256641
contig00089	2189	2870	IncFIB(AP001918)_1	0/0	100.0	96.8	AP001918	IncFIB(AP001918)_1__AP001918
contig00063	5029	5588	IncFIB(K)_1_Kpn3	0/0	100.0	98.9	JN233704	IncFIB(K)_1_Kpn3_JN233704
contig00129	574	834	IncFII_1	0/0	100.0	100.0	AY458016	IncFII_1__AY458016
contig00128	1042	1303	IncFII(pRSB107)_1_pRSB107	1/1	100.0	96.2	AJ851089	IncFII(pRSB107)_1_pRSB107_AJ851089

ID086II

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00048	3584	3725	Col156_1	0/0	92.2	98.6	NC_009781	Col156_1__NC_009781
contig00055	3142	3295	Col156_1	0/0	100.0	94.8	NC_009781	Col156_1__NC_009781
contig00035	19761	20148	IncFIA_1	0/0	100.0	99.7	AP001918	IncFIA_1__AP001918
contig00035	8473	9154	IncFIB(AP001918)_1	0/0	100.0	99.7	AP001918	IncFIB(AP001918)_1__AP001918

ID088

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00086	400	632	Col(BS512)_1	0/0	100	100.0	NC_010656	Col(BS512)_1__NC_010656
contig00054	9099	9482	IncFIA_1	0/0	99	99.7	AP001918	IncFIA_1__AP001918
contig00057	8464	9145	IncFIB(AP001918)_1	0/0	100	98.4	AP001918	IncFIB(AP001918)_1__AP001918
contig00044	8845	9218	IncX4_1	0/0	100	99.7	CP002895	IncX4_1__CP002895

ID092

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00776	3099	3486	IncFIA_1	0/0	100	99.5	AP001918	IncFIA_1__AP001918
contig00164	1832	2513	IncFIB(AP001918)_1	0/0	100	98.4	AP001918	IncFIB(AP001918)_1__AP001918
contig00772	191	451	IncFII(pRSB107)_1_pRSB107	0/0	100	100.0	AJ851089	IncFII(pRSB107)_1_pRSB107_AJ851089
contig00436	2830	3594	IncY_1	0/0	100	99.1	K02380	IncY_1__K02380

ID094LLFII

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00017	14318	14705	IncFIA_1	0/0	100	99.7	AP001918	IncFIA_1__AP001918
contig00015	1833	2514	IncFIB(AP001918)_1	0/0	100	98.4	AP001918	IncFIB(AP001918)_1__AP001918
contig00151	1238	1498	IncFII(pRSB107)_1_pRSB107	0/0	100	100.0	AJ851089	IncFII(pRSB107)_1_pRSB107_AJ851089
contig00049	87	851	IncY_1	0/0	100	99.7	K02380	IncY_1__K02380

ID099

## [1] "NO PLASMID FOUND!!"

ID09CT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00031	3158	3922	IncY_1	0/0	100	99.1	K02380	IncY_1__K02380

ID101

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00032	19680	19821	IncI1_1_Alpha	0/0	100	100	AP005147	IncI1_1_Alpha_AP005147

ID107II

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00046	14319	14706	IncFIA_1	0/0	100	99.5	AP001918	IncFIA_1__AP001918
contig00051	1833	2514	IncFIB(AP001918)_1	0/0	100	98.4	AP001918	IncFIB(AP001918)_1__AP001918
contig00069	2929	3189	IncFII(pRSB107)_1_pRSB107	0/0	100	100.0	AJ851089	IncFII(pRSB107)_1_pRSB107_AJ851089

ID124

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00051	9254	9641	IncFIA_1	0/0	100	99.7	AP001918	IncFIA_1__AP001918
contig00065	8641	9322	IncFIB(AP001918)_1	0/0	100	98.4	AP001918	IncFIB(AP001918)_1__AP001918
contig00058	3451	3711	IncFII(pAMA1167-NDM-5)_1_pAMA1167-NDM-5	0/0	100	98.1	CP024805.1	IncFII(pAMA1167-NDM-5)_1_pAMA1167-NDM-5_CP024805.1

ID127

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00044	9011	9398	IncFIA_1	0/0	100	99.7	AP001918	IncFIA_1__AP001918
contig00044	25546	26227	IncFIB(AP001918)_1	0/0	100	98.4	AP001918	IncFIB(AP001918)_1__AP001918

ID128

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00047	4077	4230	Col156_1	0/0	100	94.8	NC_009781	Col156_1__NC_009781
contig00045	5514	5644	ColRNAI_1	1/1	100	90.1	DQ298019	ColRNAI_1__DQ298019
contig00036	9281	9668	IncFIA_1	0/0	100	99.7	AP001918	IncFIA_1__AP001918
contig00021	38975	39235	IncFII_1	0/0	100	100.0	AY458016	IncFII_1__AY458016
contig00025	28681	29392	IncX4_2	0/0	100	98.7	FN543504	IncX4_2__FN543504
contig00031	8590	9354	IncY_1	0/0	100	99.1	K02380	IncY_1__K02380

ID129E

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00005	120792	121118	IncHI2_1	0/0	100	100.0	BX664015	IncHI2_1__BX664015
contig00005	135984	136613	IncHI2A_1	0/0	100	100.0	BX664015	IncHI2A_1__BX664015
contig00024	25905	26669	IncY_1	0/0	100	99.3	K02380	IncY_1__K02380

ID130

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00034	336	449	Col440I_1	0/0	100	93.9	CP023920.1	Col440I_1__CP023920.1
contig00033	3030	3794	IncY_1	0/0	100	98.8	K02380	IncY_1__K02380

ID134

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00001	99941	100267	IncHI2_1	0/0	100	100.0	BX664015	IncHI2_1__BX664015
contig00001	84446	85075	IncHI2A_1	0/0	100	100.0	BX664015	IncHI2A_1__BX664015
contig00002	25905	26669	IncY_1	0/0	100	99.3	K02380	IncY_1__K02380

ID136

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00049	3030	3794	IncY_1	0/0	100	98.8	K02380	IncY_1__K02380

ID141

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00028	95	356	Col(MG828)_1	0/0	100	93.1	NC_008486	Col(MG828)_1__NC_008486
contig00019	118	799	IncFIB(AP001918)_1	0/0	100	98.0	AP001918	IncFIB(AP001918)_1__AP001918

ID142

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00007	2910	3469	IncFIB(K)_1_Kpn3	0/0	100	91.1	JN233704	IncFIB(K)_1_Kpn3_JN233704
contig01255	258	827	IncHI1B_1_pNDM-MAR	0/0	100	99.5	JN420336	IncHI1B_1_pNDM-MAR_JN420336

ID164

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00061	8836	9219	IncFIA_1	0/0	99	99.7	AP001918	IncFIA_1__AP001918
contig00025	620	1007	IncFIA(HI1)_1_HI1	0/0	100	100.0	AF250878	IncFIA(HI1)_1_HI1_AF250878
contig00067	8471	9152	IncFIB(AP001918)_1	0/0	100	98.4	AP001918	IncFIB(AP001918)_1__AP001918
contig00032	38067	38486	IncHI1A_1	0/0	100	100.0	AF250878	IncHI1A_1__AF250878
contig00032	24451	24990	IncHI1B(R27)_1_R27	0/0	100	100.0	AF250878	IncHI1B(R27)_1_R27_AF250878

ID169

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00098	400	632	Col(BS512)_1	0/0	100.0	100.0	NC_010656	Col(BS512)_1__NC_010656
contig00066	3584	3725	Col156_1	0/0	92.2	98.6	NC_009781	Col156_1__NC_009781
contig00076	3338	3491	Col156_1	0/0	100.0	94.8	NC_009781	Col156_1__NC_009781
contig00049	19761	20148	IncFIA_1	0/0	100.0	99.7	AP001918	IncFIA_1__AP001918
contig00049	8473	9154	IncFIB(AP001918)_1	0/0	100.0	99.7	AP001918	IncFIB(AP001918)_1__AP001918

ID177

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00061	816	967	Col156_1	0/0	98.7	98.0	NC_009781	Col156_1__NC_009781
contig00062	2382	3063	IncFIB(AP001918)_1	0/0	100.0	96.8	AP001918	IncFIB(AP001918)_1__AP001918
contig00055	3388	3947	IncFIB(K)_1_Kpn3	0/0	100.0	98.9	JN233704	IncFIB(K)_1_Kpn3_JN233704
contig00034	34054	34427	IncX3_1	0/0	100.0	100.0	JN247852	IncX3_1__JN247852

ID178

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00080	400	632	Col(BS512)_1	0/0	100.0	100.0	NC_010656	Col(BS512)_1__NC_010656
contig00064	4056	4209	Col156_1	0/0	100.0	94.8	NC_009781	Col156_1__NC_009781
contig00061	3210	3320	Col440I_1	0/0	97.4	92.8	CP023920.1	Col440I_1__CP023920.1
contig00033	13744	13898	IncB/O/K/Z_2	1/1	96.2	96.1	GU256641	IncB/O/K/Z_2__GU256641
contig00041	14319	14706	IncFIA_1	0/0	100.0	99.7	AP001918	IncFIA_1__AP001918
contig00044	1448	2129	IncFIB(AP001918)_1	0/0	100.0	98.4	AP001918	IncFIB(AP001918)_1__AP001918
contig00070	377	637	IncFII(pRSB107)_1_pRSB107	0/0	100.0	100.0	AJ851089	IncFII(pRSB107)_1_pRSB107_AJ851089

ID182

## [1] "NO PLASMID FOUND!!"

ID186

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00051	1834	2515	IncFIB(AP001918)_1	0/0	100	98.4	AP001918	IncFIB(AP001918)_1__AP001918

ID187

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00073	3392	3951	IncFIB(K)_1_Kpn3	0/0	100	98.9	JN233704	IncFIB(K)_1_Kpn3_JN233704
contig00056	5945	6829	p0111_1	0/0	100	98.6	AP010962	p0111_1__AP010962

ID195

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00034	3158	3922	IncY_1	0/0	100	99.1	K02380	IncY_1__K02380

ID197

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00054	9148	9531	IncFIA_1	0/0	99	99.7	AP001918	IncFIA_1__AP001918
contig00059	8464	9145	IncFIB(AP001918)_1	0/0	100	98.4	AP001918	IncFIB(AP001918)_1__AP001918
contig00046	28680	29391	IncX4_2	0/0	100	98.9	FN543504	IncX4_2__FN543504

ID199

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00052	400	632	Col(BS512)_1	0/0	100.0	100.0	NC_010656	Col(BS512)_1__NC_010656
contig00027	3451	3838	IncFIA_1	0/0	100.0	99.7	AP001918	IncFIA_1__AP001918
contig00027	26615	27296	IncFIB(AP001918)_1	0/0	100.0	98.4	AP001918	IncFIB(AP001918)_1__AP001918
contig00048	3322	3558	IncFII(pAMA1167-NDM-5)_1_pAMA1167-NDM-5	0/0	90.8	97.9	CP024805.1	IncFII(pAMA1167-NDM-5)_1_pAMA1167-NDM-5_CP024805.1
contig00036	10337	10710	IncX1_1	0/0	100.0	94.9	EU370913	IncX1_1__EU370913

ID208

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00629	400	632	Col(BS512)_1	0/0	100	100.0	NC_010656	Col(BS512)_1__NC_010656
contig00701	1071	1332	Col(MG828)_1	0/0	100	93.1	NC_008486	Col(MG828)_1__NC_008486
contig00114	8808	9195	IncFIA_1	0/0	100	99.7	AP001918	IncFIA_1__AP001918
contig00108	1833	2514	IncFIB(AP001918)_1	0/0	100	98.4	AP001918	IncFIB(AP001918)_1__AP001918
contig00182	8871	9131	IncFII(pRSB107)_1_pRSB107	0/0	100	100.0	AJ851089	IncFII(pRSB107)_1_pRSB107_AJ851089
contig00090	10347	11111	IncY_1	0/0	100	99.9	K02380	IncY_1__K02380

ID214

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00072	5798	6181	IncFIA_1	0/0	99	99.7	AP001918	IncFIA_1__AP001918
contig00073	8464	9145	IncFIB(AP001918)_1	0/0	100	98.4	AP001918	IncFIB(AP001918)_1__AP001918
contig00057	15064	15205	IncI1_1_Alpha	0/0	100	97.9	AP005147	IncI1_1_Alpha_AP005147

ID224

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00084	1810	2071	Col(MG828)_1	0/0	100.0	93.9	NC_008486	Col(MG828)_1__NC_008486
contig00092	1033	1290	Col(MG828)_1	0/0	98.5	94.2	NC_008486	Col(MG828)_1__NC_008486
contig00074	414	620	Col8282_1	0/0	100.0	100.0	DQ995352	Col8282_1__DQ995352
contig00060	3365	3752	IncFIA_1	0/0	100.0	99.7	AP001918	IncFIA_1__AP001918
contig00067	3993	4674	IncFIB(AP001918)_1	0/0	100.0	98.4	AP001918	IncFIB(AP001918)_1__AP001918
contig00049	1	237	IncFII(pAMA1167-NDM-5)_1_pAMA1167-NDM-5	0/0	90.8	97.9	CP024805.1	IncFII(pAMA1167-NDM-5)_1_pAMA1167-NDM-5_CP024805.1
contig00045	2444	3155	IncX4_2	0/0	100.0	98.9	FN543504	IncX4_2__FN543504

ID228

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00088	400	632	Col(BS512)_1	0/0	100	100.0	NC_010656	Col(BS512)_1__NC_010656
contig00060	3338	3491	Col156_1	0/0	100	94.8	NC_009781	Col156_1__NC_009781
contig00039	18751	19138	IncFIA_1	0/0	100	99.7	AP001918	IncFIA_1__AP001918
contig00039	7463	8144	IncFIB(AP001918)_1	0/0	100	99.7	AP001918	IncFIB(AP001918)_1__AP001918
contig00064	1373	1633	IncFII_1	0/0	100	100.0	AY458016	IncFII_1__AY458016
contig00032	30264	30637	IncX1_1	0/0	100	94.7	EU370913	IncX1_1__EU370913

ID229

## [1] "NO PLASMID FOUND!!"

ID231

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00047	5286	6050	IncY_1	0/0	100	98.8	K02380	IncY_1__K02380

ID233

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00100	9396	9955	IncFIB(K)_1_Kpn3	0/0	100	91.1	JN233704	IncFIB(K)_1_Kpn3_JN233704
contig00010	29581	30019	IncFIB(Mar)_1_pNDM-Mar	0/0	100	100.0	JN420336	IncFIB(Mar)_1_pNDM-Mar_JN420336

ID235

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00081	400	632	Col(BS512)_1	0/0	100	100.0	NC_010656	Col(BS512)_1__NC_010656
contig00039	14319	14706	IncFIA_1	0/0	100	99.7	AP001918	IncFIA_1__AP001918
contig00043	1833	2514	IncFIB(AP001918)_1	0/0	100	98.4	AP001918	IncFIB(AP001918)_1__AP001918
contig00074	204	464	IncFII(pRSB107)_1_pRSB107	0/0	100	100.0	AJ851089	IncFII(pRSB107)_1_pRSB107_AJ851089

ID237

## [1] "NO PLASMID FOUND!!"

ID256

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00054	3630	3771	Col156_1	0/0	92.2	98.6	NC_009781	Col156_1__NC_009781
contig00041	10016	10697	IncFIB(AP001918)_1	0/0	100.0	96.6	AP001918	IncFIB(AP001918)_1__AP001918
contig00038	3322	3580	IncFII(29)_1_pUTI89	0/0	100.0	99.6	CP003035	IncFII(29)_1_pUTI89_CP003035
contig00025	28012	28327	IncI2_1_Delta	0/0	100.0	98.4	AP002527	IncI2_1_Delta_AP002527
contig00019	65623	66387	IncY_1	0/0	100.0	99.7	K02380	IncY_1__K02380

ID263

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00075	4074	4227	Col156_1	0/0	100	94.8	NC_009781	Col156_1__NC_009781
contig00046	9102	9489	IncFIA_1	0/0	100	99.7	AP001918	IncFIA_1__AP001918
contig00046	27503	28184	IncFIB(AP001918)_1	0/0	100	98.4	AP001918	IncFIB(AP001918)_1__AP001918
contig00064	4854	5114	IncFII(pAMA1167-NDM-5)_1_pAMA1167-NDM-5	0/0	100	98.1	CP024805.1	IncFII(pAMA1167-NDM-5)_1_pAMA1167-NDM-5_CP024805.1

ID282

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00841	1189	1302	Col440I_1	0/0	100.0	91.2	CP023920.1	Col440I_1__CP023920.1
contig00179	5514	5644	ColRNAI_1	1/1	100.0	90.1	DQ298019	ColRNAI_1__DQ298019
contig00042	14322	14684	IncFIA_1	0/0	93.6	99.7	AP001918	IncFIA_1__AP001918
contig00145	1335	2016	IncFIB(AP001918)_1	0/0	100.0	98.4	AP001918	IncFIB(AP001918)_1__AP001918
contig00008	37934	38430	IncFIC(FII)_1	1/2	99.6	95.6	AP001918	IncFIC(FII)_1__AP001918
contig00028	6293	6434	IncI1_1_Alpha	0/0	100.0	97.9	AP005147	IncI1_1_Alpha_AP005147
contig00266	261	774	IncN_1	0/0	100.0	100.0	AY046276	IncN_1__AY046276
contig00003	13402	14146	IncP1_3	0/0	100.0	100.0	KX377410	IncP1_3__KX377410
contig00013	1289	2000	IncX4_2	0/0	100.0	98.9	FN543504	IncX4_2__FN543504

ORTHO013EI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00203	1798	2440	IncFIB(pB171)_1_pB171	0/0	100	91.5	AB024946	IncFIB(pB171)_1_pB171_AB024946
contig00170	3749	3978	IncFII(Yp)_1_Yersenia	0/0	100	99.6	CP000670	IncFII(Yp)_1_Yersenia_CP000670

ORTHO055E

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00227	4351	4910	IncFIB(K)_1_Kpn3	0/0	100	98.9	JN233704	IncFIB(K)_1_Kpn3_JN233704
contig00002	22275	22713	IncFIB(Mar)_1_pNDM-Mar	0/0	100	99.3	JN420336	IncFIB(Mar)_1_pNDM-Mar_JN420336
contig00021	34348	34917	IncHI1B_1_pNDM-MAR	0/0	100	100.0	JN420336	IncHI1B_1_pNDM-MAR_JN420336
contig00145	5699	5949	IncR_1	0/0	100	100.0	DQ449578	IncR_1__DQ449578

ORTHO082EI

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00062	1798	2440	IncFIB(pB171)_1_pB171	0/0	100	91.5	AB024946	IncFIB(pB171)_1_pB171_AB024946
contig00074	2900	3129	IncFII(Yp)_1_Yersenia	0/0	100	99.6	CP000670	IncFII(Yp)_1_Yersenia_CP000670
contig00053	7870	8465	RepA_1_pKPC-CAV1321	0/0	100	100.0	CP011611	RepA_1_pKPC-CAV1321_CP011611

ORTHO08HW

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
contig00046	14320	14707	IncFIA_1	0/0	100	99.7	AP001918	IncFIA_1__AP001918
contig00047	2338	3019	IncFIB(AP001918)_1	0/0	100	98.4	AP001918	IncFIB(AP001918)_1__AP001918
contig00019	40413	41177	IncY_1	0/0	100	99.2	K02380	IncY_1__K02380

Back to index

Virulence Factor Determination

Field	Description
Contig	Contig name where the gene was found
Start	Start position of the gene within the contig
End	End position of the gene within the contig
Gene	Antibiotic resistance gene
Coverage	Proportion (%) of the gene covered
Identity	Proportion (%) of exact nucleotide matches
Accession	Accesion number of the antibiotic resistance gene
Product	Antibiotic resistance gene product

Select the sample

ID002

Contig	Start	End	Strand	Gene	Coverage	Identity	Accession	Product
contig00048	22701	23534	-	csgG	100	80.2	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00049	16600	17645	-	ompA	99	84.8	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]

ID003

Contig	Start	End	Strand	Gene	Coverage	Identity	Accession	Product
contig00021	52979	54407	+	aslA	100.0	97.1	AAG10151	(aslA) putative arylsulfatase [AslA (VF0238)] [Escherichia coli O18:K1:H7 str. RS218]
contig00029	36588	37616	-	chuS	100.0	96.4	NP_756169	(chuS) heme oxygenase ChuS [Chu (VF0227)] [Escherichia coli CFT073]
contig00029	43780	44772	+	chuU	100.0	96.6	NP_756179	(chuU) heme permease protein ChuU [Chu (VF0227)] [Escherichia coli CFT073]
contig00029	44739	45539	+	chuV	100.0	98.1	NP_756180	(chuV) ATP-binding hydrophilic protein ChuV [Chu (VF0227)] [Escherichia coli CFT073]
contig00029	41264	42601	+	chuW	100.0	96.8	NP_756176	(chuW) Putative oxygen independent coproporphyrinogen III oxidase [Chu (VF0227)] [Escherichia coli CFT073]
contig00029	43108	43731	+	chuY	100.0	96.5	NP_756178	(chuY) ChuY [Chu (VF0227)] [Escherichia coli CFT073]
contig00003	94251	94706	-	csgB	99.8	83.6	NP_460114	(csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00003	95461	96111	+	csgD	100.0	81.4	NP_460113	(csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00003	96530	96946	+	csgF	99.0	81.0	NP_460111	(csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00003	96973	97806	+	csgG	100.0	83.3	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00014	87719	88465	-	entA	100.0	97.3	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00014	88465	89322	-	entB	100.0	98.8	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00014	90956	92143	-	entC	100.0	97.3	NP_752611	(entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00014	106600	107370	+	entD	100.0	92.7	NP_752599	(entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00014	89336	90946	-	entE	100.0	96.5	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00014	98819	102672	-	entF	99.2	95.2	NP_752604	(entF) enterobactin synthase multienzyme complex component ATP-dependent [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00014	93280	94530	-	entS	100.0	95.7	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00004	3737	5635	+	espL1	100.0	96.3	NP_288154	(espL1) Type III secretion system effector espL1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00006	6763	8949	-	espL4	100.0	97.4	NP_290644	(espL4) Type III secretion system effector EspL4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00034	8773	10025	+	espR1	99.4	94.2	NP_287686	(espR1) Type III secretion system effector espR1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00004	215089	216197	-	espR4	97.2	84.6	NP_288396	(espR4) Type III secretion system effector espR4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00007	87915	89336	+	espX1	100.0	96.0	NP_285716	(espX1) Type III secretion system effector EspX1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00006	41231	42811	+	espX4	100.0	95.9	NP_290672	(espX4) Type III secretion system effector EspX4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00006	72307	73599	-	espX5	100.0	95.8	NP_290699	(espX5) Type III secretion system effector EspX5 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00007	48462	49228	-	espY1	99.9	93.9	NP_285753	(espY1) Type III secretion system effector EspY1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00007	31446	31996	-	espY2	96.5	88.8	NP_285765	(espY2) Type III secretion system effector EspY2 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00031	31377	32948	+	espY3	100.0	95.5	NP_286160	(espY3) Type III secretion system effector EspY3 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00017	39565	41973	+	espY4	100.0	96.4	NP_290352	(espY4) Type III secretion system effector EspY4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00009	106407	110657	-	fdeC	100.0	95.2	YP_002390132	(fdeC) adhesin FdeC [FdeC (VF0506)] [Escherichia coli O45:K1:H7 str. S88]
contig00014	104335	106575	+	fepA	100.0	96.9	NP_752600	(fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00014	92320	93276	+	fepB	100.0	97.7	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00014	96631	97446	+	fepC	100.0	96.9	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00014	94629	95645	+	fepD	100.0	96.0	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00014	95642	96634	+	fepG	100.0	94.1	NP_752607	(fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00014	102890	104092	-	fes	100.0	96.8	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00007	195230	195841	-	fimA	100.0	88.4	NP_757241	(fimA) Type-1 fimbrial protein A chain precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00025	76002	76604	+	fimB	100.0	98.0	NP_757239	(fimB) Type 1 fimbriae Regulatory protein fimB [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00007	193864	194589	-	fimC	100.0	98.6	NP_757243	(fimC) Chaperone protein fimC precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00007	191161	193797	-	fimD	100.0	98.5	NP_757244	(fimD) Outer membrane usher protein fimD precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00025	77081	77675	+	fimE	99.7	99.3	NP_757240	(fimE) Type 1 fimbriae Regulatory protein fimE [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00007	190621	191154	-	fimF	100.0	97.8	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00007	190105	190608	-	fimG	100.0	98.0	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00007	189183	190094	-	fimH	100.0	97.3	NP_757248	(fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00007	194626	195165	-	fimI	100.0	98.9	NP_757242	(fimI) Fimbrin-like protein fimI precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00001	199441	200271	-	gspC	100.0	95.1	YP_404599	(gspC) general secretion pathway protein C [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	197351	199201	-	gspD	100.0	96.2	YP_404600	(gspD) general secretion pathway protein D [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	195858	197351	-	gspE	100.0	95.8	YP_404601	(gspE) general secretion pathway protein E [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	194659	195858	-	gspF	100.0	94.9	YP_404602	(gspF) general secretion pathway protein F [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	194163	194618	-	gspG	100.0	95.8	YP_404603	(gspG) general secretion pathway protein G [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	193596	194126	-	gspH	100.0	95.3	YP_404604	(gspH) general secretion pathway protein H [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	193228	193599	-	gspI	100.0	96.2	YP_404605	(gspI) general secretion pathway protein I [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	192626	193195	-	gspJ	100.0	95.3	YP_404606	(gspJ) general secretion pathway protein J [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	191652	192629	-	gspK	100.0	97.4	YP_404607	(gspK) general secretion pathway protein K [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	190477	191337	-	gspL	100.0	95.8	YP_404608	(gspL) general secretion pathway protein L [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	189940	190361	-	gspM	99.8	94.5	YP_404609	(gspM) general secretion pathway protein M [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	175110	176786	+	kpsD	100.0	98.1	AAA21682	(kpsD) KpsD [K1 capsule (VF0239)] [Escherichia coli O18:K1:H7 str. RS218]
contig00003	166279	167331	+	ompA	100.0	95.2	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00001	157773	158323	+	papX	99.6	80.7	NP_755457	(papX) PapX protein regulates flagellum synthesis to repress motility [P fimbriae (CVF425)] [Escherichia coli CFT073]
contig00029	37665	39647	-	shuA	100.0	98.5	YP_405019	(shuA) outer membrane heme/hemoglobin receptor ShuA [Shu (VF0256)] [Shigella dysenteriae Sd197]
contig00029	40252	41244	+	shuT	100.0	98.1	YP_405017	(shuT) periplasmic binding protein ShuT [Shu (VF0256)] [Shigella dysenteriae Sd197]
contig00029	42614	43108	+	shuX	100.0	96.4	YP_405016	(shuX) shu locus protein ShuX [Shu (VF0256)] [Shigella dysenteriae Sd197]
contig00009	125988	126741	+	yagV/ecpE	99.7	97.9	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00009	124421	126064	+	yagW/ecpD	100.0	98.9	NP_286007	(yagW/ecpD) polymerized tip adhesin of ECP fibers [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00009	121906	124431	+	yagX/ecpC	100.0	98.0	NP_286008	(yagX/ecpC) E. coli common pilus usher EcpC [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00009	121212	121880	+	yagY/ecpB	100.0	97.5	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00009	120568	121155	+	yagZ/ecpA	100.0	99.0	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00009	119903	120493	+	ykgK/ecpR	100.0	99.0	NP_286011	(ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

ID005

Contig	Start	End	Strand	Gene	Coverage	Identity	Accession	Product
contig00054	8158	8508	-	aap/aspU	100.0	98.0	YP_006099176	(aap/aspU) Dispersin [Dispersin (VF0215)] [Escherichia coli O44:H18 042]
contig00039	38755	39270	+	aggA	100.0	85.7	AAA57454	(aggA) fimbrial major subunit [AAFs (VF0214)] [Escherichia coli 17-2]
contig00039	38217	38654	+	aggB	100.0	98.2	AAA57453	(aggB) fimbrial minor subunit [AAFs (VF0214)] [Escherichia coli 17-2]
contig00039	35675	38203	+	aggC	100.0	99.7	AAA57452	(aggC) usher protein [AAFs (VF0214)] [Escherichia coli 17-2]
contig00039	34903	35661	+	aggD	100.0	99.6	AAA57451	(aggD) chaperone [AAFs (VF0214)] [Escherichia coli 17-2]
contig00023	53224	54652	+	aslA	100.0	97.1	AAG10151	(aslA) putative arylsulfatase [AslA (VF0238)] [Escherichia coli O18:K1:H7 str. RS218]
contig00020	74060	75088	+	chuS	100.0	96.4	NP_756169	(chuS) heme oxygenase ChuS [Chu (VF0227)] [Escherichia coli CFT073]
contig00020	66904	67896	-	chuU	100.0	96.6	NP_756179	(chuU) heme permease protein ChuU [Chu (VF0227)] [Escherichia coli CFT073]
contig00020	66137	66937	-	chuV	100.0	98.2	NP_756180	(chuV) ATP-binding hydrophilic protein ChuV [Chu (VF0227)] [Escherichia coli CFT073]
contig00020	69075	70412	-	chuW	100.0	96.8	NP_756176	(chuW) Putative oxygen independent coproporphyrinogen III oxidase [Chu (VF0227)] [Escherichia coli CFT073]
contig00020	67945	68568	-	chuY	100.0	96.5	NP_756178	(chuY) ChuY [Chu (VF0227)] [Escherichia coli CFT073]
contig00021	83214	83669	-	csgB	99.8	83.6	NP_460114	(csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00021	84424	85074	+	csgD	100.0	81.4	NP_460113	(csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00021	85493	85909	+	csgF	99.0	81.0	NP_460111	(csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00021	85936	86769	+	csgG	100.0	83.3	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00014	87837	88583	-	entA	100.0	97.3	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00014	88583	89440	-	entB	100.0	98.8	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00014	91074	92261	-	entC	100.0	97.3	NP_752611	(entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00014	106719	107489	+	entD	100.0	92.7	NP_752599	(entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00014	89454	91064	-	entE	100.0	96.5	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00014	98938	102791	-	entF	99.3	95.5	NP_752604	(entF) enterobactin synthase multienzyme complex component ATP-dependent [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00014	93398	94648	-	entS	100.0	95.7	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00001	13790	15688	+	espL1	100.0	96.3	NP_288154	(espL1) Type III secretion system effector espL1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00005	6763	8949	-	espL4	100.0	97.4	NP_290644	(espL4) Type III secretion system effector EspL4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00045	8773	10025	+	espR1	99.4	94.3	NP_287686	(espR1) Type III secretion system effector espR1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00001	220396	221531	-	espR4	99.6	84.5	NP_288396	(espR4) Type III secretion system effector espR4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00013	91169	92590	-	espX1	100.0	96.0	NP_285716	(espX1) Type III secretion system effector EspX1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00005	41231	42811	+	espX4	100.0	95.9	NP_290672	(espX4) Type III secretion system effector EspX4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00005	72307	73599	-	espX5	100.0	95.9	NP_290699	(espX5) Type III secretion system effector EspX5 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00013	131277	132010	+	espY1	97.5	93.9	NP_285753	(espY1) Type III secretion system effector EspY1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00010	145208	145777	-	espY2	100.0	94.6	NP_285765	(espY2) Type III secretion system effector EspY2 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00041	31222	32793	+	espY3	100.0	95.4	NP_286160	(espY3) Type III secretion system effector EspY3 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00022	19207	21615	+	espY4	100.0	96.4	NP_290352	(espY4) Type III secretion system effector EspY4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00009	106396	110646	-	fdeC	100.0	95.2	YP_002390132	(fdeC) adhesin FdeC [FdeC (VF0506)] [Escherichia coli O45:K1:H7 str. S88]
contig00014	104454	106694	+	fepA	100.0	96.9	NP_752600	(fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00014	92438	93394	+	fepB	100.0	97.7	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00014	96749	97564	+	fepC	100.0	96.9	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00014	94747	95763	+	fepD	100.0	96.0	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00014	95760	96752	+	fepG	100.0	94.2	NP_752607	(fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00014	103009	104211	-	fes	100.0	96.6	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00035	17433	18263	+	gspC	100.0	95.2	YP_404599	(gspC) general secretion pathway protein C [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00035	18503	20353	+	gspD	100.0	96.1	YP_404600	(gspD) general secretion pathway protein D [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00035	20353	21846	+	gspE	100.0	95.0	YP_404601	(gspE) general secretion pathway protein E [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00035	21846	23045	+	gspF	100.0	94.2	YP_404602	(gspF) general secretion pathway protein F [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00035	23086	23541	+	gspG	100.0	96.0	YP_404603	(gspG) general secretion pathway protein G [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00035	23578	24108	+	gspH	100.0	94.7	YP_404604	(gspH) general secretion pathway protein H [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00035	24105	24476	+	gspI	100.0	92.2	YP_404605	(gspI) general secretion pathway protein I [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00035	24509	25078	+	gspJ	100.0	94.4	YP_404606	(gspJ) general secretion pathway protein J [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00035	25075	26052	+	gspK	100.0	96.5	YP_404607	(gspK) general secretion pathway protein K [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00035	26367	27227	+	gspL	100.0	94.8	YP_404608	(gspL) general secretion pathway protein L [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00035	27343	27764	+	gspM	99.8	92.7	YP_404609	(gspM) general secretion pathway protein M [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00035	42485	44161	-	kpsD	100.0	98.3	AAA21682	(kpsD) KpsD [K1 capsule (VF0239)] [Escherichia coli O18:K1:H7 str. RS218]
contig00035	28823	29599	+	kpsM	100.0	94.8	AAA24046	(kpsM) KpsM [K1 capsule (VF0239)] [Escherichia coli O18:K1:H7 str. RS218]
contig00006	88637	89689	+	ompA	100.0	95.2	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00020	72029	74011	+	shuA	100.0	98.5	YP_405019	(shuA) outer membrane heme/hemoglobin receptor ShuA [Shu (VF0256)] [Shigella dysenteriae Sd197]
contig00020	70432	71424	-	shuT	100.0	98.1	YP_405017	(shuT) periplasmic binding protein ShuT [Shu (VF0256)] [Shigella dysenteriae Sd197]
contig00020	68568	69062	-	shuX	100.0	96.4	YP_405016	(shuX) shu locus protein ShuX [Shu (VF0256)] [Shigella dysenteriae Sd197]
contig00009	125978	126731	+	yagV/ecpE	99.7	97.0	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00009	124411	126054	+	yagW/ecpD	100.0	99.2	NP_286007	(yagW/ecpD) polymerized tip adhesin of ECP fibers [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00009	121896	124421	+	yagX/ecpC	100.0	98.0	NP_286008	(yagX/ecpC) E. coli common pilus usher EcpC [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00009	121202	121870	+	yagY/ecpB	100.0	98.5	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00009	120558	121145	+	yagZ/ecpA	100.0	99.0	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00009	119893	120483	+	ykgK/ecpR	100.0	99.0	NP_286011	(ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

ID006

Contig	Start	End	Strand	Gene	Coverage	Identity	Accession	Product
contig00094	630	1085	-	csgB	99.8	83.6	NP_460114	(csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00094	1839	2489	+	csgD	100.0	81.3	NP_460113	(csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00094	2908	3324	+	csgF	99.0	81.2	NP_460111	(csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00094	3351	4184	+	csgG	100.0	83.3	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00052	7812	8558	-	entA	100.0	95.7	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00052	8558	9415	-	entB	100.0	98.1	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00052	11049	12236	-	entC	100.0	97.9	NP_752611	(entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00052	26880	27650	+	entD	100.0	94.3	NP_752599	(entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00052	9429	11039	-	entE	100.0	95.5	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00052	19099	22952	-	entF	99.3	95.6	NP_752604	(entF) enterobactin synthase multienzyme complex component ATP-dependent [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00052	13559	14809	-	entS	100.0	95.4	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00048	11028	12083	+	espR1	83.8	94.1	NP_287686	(espR1) Type III secretion system effector espR1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00033	24119	25699	-	espX4	99.9	93.0	NP_290672	(espX4) Type III secretion system effector EspX4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00042	5443	6736	-	espX5	100.0	95.8	NP_290699	(espX5) Type III secretion system effector EspX5 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00096	2533	6537	-	fdeC	93.9	93.7	YP_002390132	(fdeC) adhesin FdeC [FdeC (VF0506)] [Escherichia coli O45:K1:H7 str. S88]
contig00052	24615	26855	+	fepA	100.0	96.8	NP_752600	(fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00052	12599	13555	+	fepB	100.0	97.5	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00052	16910	17725	+	fepC	100.0	97.3	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00052	14908	15924	+	fepD	100.0	96.2	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00052	15921	16913	+	fepG	100.0	94.0	NP_752607	(fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00052	23170	24372	-	fes	100.0	96.6	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00079	11874	12479	-	fimA	100.0	95.4	NP_757241	(fimA) Type-1 fimbrial protein A chain precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00106	1427	2029	-	fimB	100.0	98.0	NP_757239	(fimB) Type 1 fimbriae Regulatory protein fimB [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00079	10509	11234	-	fimC	100.0	99.2	NP_757243	(fimC) Chaperone protein fimC precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00079	7806	10442	-	fimD	100.0	98.8	NP_757244	(fimD) Outer membrane usher protein fimD precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00106	353	949	-	fimE	100.0	98.5	NP_757240	(fimE) Type 1 fimbriae Regulatory protein fimE [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00079	7266	7799	-	fimF	100.0	99.1	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00079	6750	7253	-	fimG	100.0	98.2	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00079	5828	6739	-	fimH	100.0	97.5	NP_757248	(fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00079	11271	11809	-	fimI	99.8	98.5	NP_757242	(fimI) Fimbrin-like protein fimI precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00041	3	982	+	gspF	81.7	95.6	YP_404602	(gspF) general secretion pathway protein F [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00041	1023	1478	+	gspG	100.0	95.0	YP_404603	(gspG) general secretion pathway protein G [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00041	1515	2045	+	gspH	100.0	95.5	YP_404604	(gspH) general secretion pathway protein H [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00041	2042	2413	+	gspI	100.0	95.2	YP_404605	(gspI) general secretion pathway protein I [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00041	2446	3015	+	gspJ	100.0	96.5	YP_404606	(gspJ) general secretion pathway protein J [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00041	3012	3989	+	gspK	100.0	96.7	YP_404607	(gspK) general secretion pathway protein K [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00041	4304	5164	+	gspL	100.0	97.1	YP_404608	(gspL) general secretion pathway protein L [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00041	5280	5702	+	gspM	100.0	98.3	YP_404609	(gspM) general secretion pathway protein M [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00005	103804	104844	-	ompA	100.0	98.1	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]

ID007I

Contig	Start	End	Strand	Gene	Coverage	Identity	Accession	Product
contig00018	71083	72511	+	aslA	100.0	98.2	AAG10151	(aslA) putative arylsulfatase [AslA (VF0238)] [Escherichia coli O18:K1:H7 str. RS218]
contig00058	16900	18561	+	chuA	85.4	99.6	NP_756170	(chuA) Outer membrane heme/hemoglobin receptor ChuA [Chu (VF0227)] [Escherichia coli CFT073]
contig00007	171049	172077	-	chuS	100.0	99.0	NP_756169	(chuS) heme oxygenase ChuS [Chu (VF0227)] [Escherichia coli CFT073]
contig00058	15266	16258	-	chuT	100.0	99.8	NP_756175	(chuT) periplasmic heme-binding protein ChuT [Chu (VF0227)] [Escherichia coli CFT073]
contig00058	11738	12730	-	chuU	100.0	99.5	NP_756179	(chuU) heme permease protein ChuU [Chu (VF0227)] [Escherichia coli CFT073]
contig00058	10971	11771	-	chuV	100.0	99.8	NP_756180	(chuV) ATP-binding hydrophilic protein ChuV [Chu (VF0227)] [Escherichia coli CFT073]
contig00058	13909	15246	-	chuW	100.0	98.9	NP_756176	(chuW) Putative oxygen independent coproporphyrinogen III oxidase [Chu (VF0227)] [Escherichia coli CFT073]
contig00058	13402	13896	-	chuX	100.0	99.8	NP_756177	(chuX) putative heme-binding protein ChuX [Chu (VF0227)] [Escherichia coli CFT073]
contig00058	12779	13402	-	chuY	100.0	98.2	NP_756178	(chuY) ChuY [Chu (VF0227)] [Escherichia coli CFT073]
contig00016	102979	103434	-	csgB	99.8	83.8	NP_460114	(csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00016	104187	104837	+	csgD	100.0	81.6	NP_460113	(csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00016	105256	105672	+	csgF	99.0	80.8	NP_460111	(csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00016	105699	106532	+	csgG	100.0	83.2	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00017	99291	100037	-	entA	100.0	98.1	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00017	100037	100894	-	entB	100.0	99.4	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00017	102528	103715	-	entC	100.0	98.7	NP_752611	(entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00062	6354	7015	-	entD	85.9	96.7	NP_752599	(entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00017	100908	102518	-	entE	100.0	98.9	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00062	10943	14824	+	entF	100.0	98.2	NP_752604	(entF) enterobactin synthase multienzyme complex component ATP-dependent [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00017	104852	106102	-	entS	100.0	97.4	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00045	22455	26702	-	fdeC	99.9	97.4	YP_002390132	(fdeC) adhesin FdeC [FdeC (VF0506)] [Escherichia coli O45:K1:H7 str. S88]
contig00062	7040	9280	-	fepA	100.0	98.9	NP_752600	(fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00017	103892	104848	+	fepB	100.0	98.4	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00017	108203	109018	+	fepC	100.0	99.1	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00017	106201	107217	+	fepD	100.0	97.8	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00017	107214	108206	+	fepG	100.0	97.9	NP_752607	(fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00062	9523	10725	+	fes	100.0	99.0	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00053	12960	13564	-	fimA	99.8	90.8	NP_757241	(fimA) Type-1 fimbrial protein A chain precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00053	11594	12319	-	fimC	100.0	98.9	NP_757243	(fimC) Chaperone protein fimC precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00053	8891	11527	-	fimD	100.0	98.5	NP_757244	(fimD) Outer membrane usher protein fimD precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00053	13987	14583	-	fimE	100.0	98.8	NP_757240	(fimE) Type 1 fimbriae Regulatory protein fimE [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00053	8351	8884	-	fimF	100.0	96.6	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00053	7835	8338	-	fimG	100.0	98.2	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00053	6913	7824	-	fimH	100.0	97.5	NP_757248	(fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00053	12356	12895	-	fimI	100.0	98.5	NP_757242	(fimI) Fimbrin-like protein fimI precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00025	32621	34642	-	fyuA	100.0	99.8	NP_405467	(fyuA) pesticin/yersiniabactin receptor protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00009	14199	15029	-	gspC	100.0	95.3	YP_404599	(gspC) general secretion pathway protein C [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00009	12109	13959	-	gspD	100.0	96.0	YP_404600	(gspD) general secretion pathway protein D [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00009	10616	12109	-	gspE	100.0	95.2	YP_404601	(gspE) general secretion pathway protein E [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00009	9417	10616	-	gspF	100.0	95.4	YP_404602	(gspF) general secretion pathway protein F [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00009	8921	9376	-	gspG	100.0	95.8	YP_404603	(gspG) general secretion pathway protein G [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00009	8354	8884	-	gspH	100.0	95.5	YP_404604	(gspH) general secretion pathway protein H [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00009	7986	8357	-	gspI	100.0	94.4	YP_404605	(gspI) general secretion pathway protein I [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00009	7384	7953	-	gspJ	100.0	96.0	YP_404606	(gspJ) general secretion pathway protein J [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00009	6410	7387	-	gspK	100.0	97.4	YP_404607	(gspK) general secretion pathway protein K [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00009	5235	6095	-	gspL	100.0	94.7	YP_404608	(gspL) general secretion pathway protein L [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00009	4698	5119	-	gspM	99.8	91.9	YP_404609	(gspM) general secretion pathway protein M [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00025	38251	47742	-	irp1	100.0	99.8	NP_405471	(irp1) yersiniabactin biosynthetic protein Irp1 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00025	47830	53937	-	irp2	100.0	99.5	NP_405472	(irp2) yersiniabactin biosynthetic protein Irp2 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00055	8834	10615	+	iucA	100.0	99.8	NP_709454	(iucA) aerobactin synthesis protein IucA [Aerobactin (VF0123)] [Shigella flexneri 2a str. 301]
contig00055	10616	11563	+	iucB	100.0	99.8	NP_709455	(iucB) aerobactin synthesis protein IucB [Aerobactin (VF0123)] [Shigella flexneri 2a str. 301]
contig00055	11563	13305	+	iucC	100.0	98.2	NP_755500	(iucC) aerobactin siderophore biosynthesis protein IucC [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00055	13302	14623	+	iucD	98.8	96.3	NP_755499	(iucD) L-lysine 6-monooxygenase IucD [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00055	14561	16862	+	iutA	100.0	88.4	NP_755498	(iutA) ferric aerobactin receptor precusor IutA [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00042	6403	8079	-	kpsD	100.0	98.3	AAA21682	(kpsD) KpsD [K1 capsule (VF0239)] [Escherichia coli O18:K1:H7 str. RS218]
contig00009	2859	3635	-	kpsM	100.0	94.5	AAA24046	(kpsM) KpsM [K1 capsule (VF0239)] [Escherichia coli O18:K1:H7 str. RS218]
contig00004	59575	60627	+	ompA	100.0	95.8	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00055	748	1061	-	papB	99.7	98.4		(papB) regulatory protein PapB [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig00055	1466	1699	+	papI	100.0	94.9	NP_755468	(papI) regulatory protein PapI [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig00140	256	807	+	papX	100.0	97.6	NP_755457	(papX) PapX protein regulates flagellum synthesis to repress motility [P fimbriae (CVF425)] [Escherichia coli CFT073]
contig00055	17794	21693	+	sat	100.0	99.6	NP_755494	(sat) Aecreted auto transpoter toxin [Sat (VF0231)] [Escherichia coli CFT073]
contig00070	5186	6324	+	senB	99.9	99.7	YP_406304	(senB) enterotoxin [ShET2 (VF0258)] [Shigella flexneri 2a str. 301]
contig00022	11788	12541	+	yagV/ecpE	99.7	98.0	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00022	10221	11864	+	yagW/ecpD	100.0	99.2	NP_286007	(yagW/ecpD) polymerized tip adhesin of ECP fibers [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00022	7706	10231	+	yagX/ecpC	100.0	97.6	NP_286008	(yagX/ecpC) E. coli common pilus usher EcpC [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00022	7012	7680	+	yagY/ecpB	100.0	98.1	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00022	6368	6955	+	yagZ/ecpA	100.0	98.5	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00025	54128	55087	-	ybtA	100.0	99.3	NP_405473	(ybtA) transcriptional regulator YbtA [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00025	34773	36350	-	ybtE	100.0	99.8	NP_405468	(ybtE) yersiniabactin siderophore biosynthetic protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00025	55254	57056	+	ybtP	100.0	99.6	NP_405474	(ybtP) lipoprotein inner membrane ABC-transporter [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00025	57043	58845	+	ybtQ	100.0	99.6	NP_405475	(ybtQ) inner membrane ABC-transporter YbtQ [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00025	60146	61450	+	ybtS	100.0	99.8	NP_405477	(ybtS) salicylate synthase Irp9 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00025	36354	37157	-	ybtT	100.0	99.6	NP_405469	(ybtT) yersiniabactin biosynthetic protein YbtT [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00025	37154	38254	-	ybtU	100.0	99.7	NP_405470	(ybtU) yersiniabactin biosynthetic protein YbtU [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00025	58838	60118	+	ybtX	100.0	99.7	NP_405476	(ybtX) putative signal transducer [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00022	5703	6293	+	ykgK/ecpR	100.0	99.5	NP_286011	(ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

ID011

Contig	Start	End	Strand	Gene	Coverage	Identity	Accession	Product
contig00022	73372	73677	-	afaA	100.0	100.0	CAW30797	(afaA) fimbrial major subunit AfaA [Afimbrial adhesin AFA-I mannose-resistant adhesin (AI010)] [Escherichia coli O25b:H4 str. FV9863]
contig00022	72344	73088	-	afaB-I	100.0	99.6	CAW30798	(afaB-I) chaperone AfaB [Afimbrial adhesin AFA-I mannose-resistant adhesin (AI010)] [Escherichia coli O25b:H4 str. FV9863]
contig00022	69669	72251	-	afaC-I	100.0	99.9	CAW30799	(afaC-I) usher AfaC [Afimbrial adhesin AFA-I mannose-resistant adhesin (AI010)] [Escherichia coli O25b:H4 str. FV9863]
contig00022	69210	69653	-	afaD	100.0	100.0	CAW30800	(afaD) AfaD [Afimbrial adhesin AFA-I mannose-resistant adhesin (AI010)] [Escherichia coli O25b:H4 str. FV9863]
contig00022	67972	68457	-	afaE-I	100.0	99.8	CAW30801	(afaE-I) AFA-I adhesin [Afa/Dr family (VF0212)] [Escherichia coli O25b:H4 str. FV9863]
contig00018	71089	72517	+	aslA	100.0	98.2	AAG10151	(aslA) putative arylsulfatase [AslA (VF0238)] [Escherichia coli O18:K1:H7 str. RS218]
contig00008	172126	174072	-	chuA	100.0	99.5	NP_756170	(chuA) Outer membrane heme/hemoglobin receptor ChuA [Chu (VF0227)] [Escherichia coli CFT073]
contig00008	171049	172077	-	chuS	100.0	99.0	NP_756169	(chuS) heme oxygenase ChuS [Chu (VF0227)] [Escherichia coli CFT073]
contig00008	174714	175706	+	chuT	100.0	99.8	NP_756175	(chuT) periplasmic heme-binding protein ChuT [Chu (VF0227)] [Escherichia coli CFT073]
contig00008	178242	179234	+	chuU	100.0	99.5	NP_756179	(chuU) heme permease protein ChuU [Chu (VF0227)] [Escherichia coli CFT073]
contig00008	179201	180001	+	chuV	100.0	99.8	NP_756180	(chuV) ATP-binding hydrophilic protein ChuV [Chu (VF0227)] [Escherichia coli CFT073]
contig00008	175726	177063	+	chuW	100.0	98.9	NP_756176	(chuW) Putative oxygen independent coproporphyrinogen III oxidase [Chu (VF0227)] [Escherichia coli CFT073]
contig00008	177076	177570	+	chuX	100.0	100.0	NP_756177	(chuX) putative heme-binding protein ChuX [Chu (VF0227)] [Escherichia coli CFT073]
contig00008	177570	178193	+	chuY	100.0	98.2	NP_756178	(chuY) ChuY [Chu (VF0227)] [Escherichia coli CFT073]
contig00011	102874	103329	-	csgB	99.8	83.8	NP_460114	(csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00011	104082	104732	+	csgD	100.0	81.6	NP_460113	(csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00011	105151	105567	+	csgF	99.0	80.8	NP_460111	(csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00011	105594	106427	+	csgG	100.0	83.2	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00022	74595	74822	+	daaF	100.0	100.0	AAA23662	(daaF) DaaF protein [F1845 fimbrial adhesin (AI016)] [Escherichia coli str. C1845]
contig00022	68659	68832	-	draP	100.0	98.8	AAK16479	(draP) DraP [Dr adhesins (VF0223)] [Escherichia coli O75:K5:H- str. IH11128]
contig00002	150203	150949	-	entA	100.0	98.1	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00002	150949	151806	-	entB	100.0	99.4	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00002	153440	154627	-	entC	100.0	98.7	NP_752611	(entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00002	169116	169777	+	entD	85.9	96.7	NP_752599	(entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00002	151820	153430	-	entE	100.0	98.9	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00002	161307	165188	-	entF	100.0	98.2	NP_752604	(entF) enterobactin synthase multienzyme complex component ATP-dependent [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00002	155764	157014	-	entS	100.0	97.4	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00002	442080	446327	-	fdeC	99.9	97.4	YP_002390132	(fdeC) adhesin FdeC [FdeC (VF0506)] [Escherichia coli O45:K1:H7 str. S88]
contig00002	166851	169091	+	fepA	100.0	98.9	NP_752600	(fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00002	154804	155760	+	fepB	100.0	98.4	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00002	159115	159930	+	fepC	100.0	99.1	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00002	157113	158129	+	fepD	100.0	97.8	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00002	158126	159118	+	fepG	100.0	97.9	NP_752607	(fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00002	165406	166608	-	fes	100.0	99.0	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00003	331451	332055	-	fimA	99.8	90.8	NP_757241	(fimA) Type-1 fimbrial protein A chain precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00003	330085	330810	-	fimC	100.0	98.9	NP_757243	(fimC) Chaperone protein fimC precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00003	327382	330018	-	fimD	100.0	98.5	NP_757244	(fimD) Outer membrane usher protein fimD precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00003	332478	333074	-	fimE	100.0	98.8	NP_757240	(fimE) Type 1 fimbriae Regulatory protein fimE [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00003	326842	327375	-	fimF	100.0	96.6	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00003	326326	326829	-	fimG	100.0	98.2	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00003	325404	326315	-	fimH	100.0	97.5	NP_757248	(fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00003	330847	331386	-	fimI	100.0	98.5	NP_757242	(fimI) Fimbrin-like protein fimI precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00027	41502	43523	-	fyuA	100.0	99.8	NP_405467	(fyuA) pesticin/yersiniabactin receptor protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00007	167409	168239	+	gspC	100.0	93.9	YP_404599	(gspC) general secretion pathway protein C [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00007	168479	170329	+	gspD	100.0	96.1	YP_404600	(gspD) general secretion pathway protein D [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00007	170329	171822	+	gspE	100.0	95.0	YP_404601	(gspE) general secretion pathway protein E [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00007	171822	173021	+	gspF	100.0	94.2	YP_404602	(gspF) general secretion pathway protein F [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00007	173062	173517	+	gspG	100.0	96.0	YP_404603	(gspG) general secretion pathway protein G [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00007	173554	174084	+	gspH	100.0	94.7	YP_404604	(gspH) general secretion pathway protein H [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00007	174081	174452	+	gspI	100.0	92.2	YP_404605	(gspI) general secretion pathway protein I [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00007	174485	175054	+	gspJ	100.0	94.4	YP_404606	(gspJ) general secretion pathway protein J [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00007	175051	176028	+	gspK	100.0	96.6	YP_404607	(gspK) general secretion pathway protein K [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00007	176343	177203	+	gspL	100.0	94.8	YP_404608	(gspL) general secretion pathway protein L [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00007	177319	177740	+	gspM	99.8	92.9	YP_404609	(gspM) general secretion pathway protein M [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00036	11815	17922	+	irp2	100.0	99.4	NP_405472	(irp2) yersiniabactin biosynthetic protein Irp2 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00035	8835	10616	+	iucA	100.0	99.8	NP_709454	(iucA) aerobactin synthesis protein IucA [Aerobactin (VF0123)] [Shigella flexneri 2a str. 301]
contig00035	10617	11564	+	iucB	100.0	99.8	NP_709455	(iucB) aerobactin synthesis protein IucB [Aerobactin (VF0123)] [Shigella flexneri 2a str. 301]
contig00035	11564	13306	+	iucC	100.0	98.2	NP_755500	(iucC) aerobactin siderophore biosynthesis protein IucC [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00035	13303	14624	+	iucD	98.8	96.3	NP_755499	(iucD) L-lysine 6-monooxygenase IucD [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00035	14562	16863	+	iutA	100.0	88.4	NP_755498	(iutA) ferric aerobactin receptor precusor IutA [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00007	192461	194137	-	kpsD	100.0	98.3	AAA21682	(kpsD) KpsD [K1 capsule (VF0239)] [Escherichia coli O18:K1:H7 str. RS218]
contig00007	178799	179575	+	kpsM	100.0	94.7	AAA24046	(kpsM) KpsM [K1 capsule (VF0239)] [Escherichia coli O18:K1:H7 str. RS218]
contig00015	1055	2107	+	ompA	100.0	95.8	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00035	749	1062	-	papB	99.7	98.4		(papB) regulatory protein PapB [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig00035	1467	1700	+	papI	100.0	94.9	NP_755468	(papI) regulatory protein PapI [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig00070	763	1314	+	papX	100.0	97.6	NP_755457	(papX) PapX protein regulates flagellum synthesis to repress motility [P fimbriae (CVF425)] [Escherichia coli CFT073]
contig00035	17795	21694	+	sat	100.0	99.6	NP_755494	(sat) Aecreted auto transpoter toxin [Sat (VF0231)] [Escherichia coli CFT073]
contig00047	7702	8840	+	senB	99.9	99.7	YP_406304	(senB) enterotoxin [ShET2 (VF0258)] [Shigella flexneri 2a str. 301]
contig00002	461665	462418	+	yagV/ecpE	99.7	98.0	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00002	460098	461741	+	yagW/ecpD	100.0	99.2	NP_286007	(yagW/ecpD) polymerized tip adhesin of ECP fibers [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00002	457583	460108	+	yagX/ecpC	100.0	97.6	NP_286008	(yagX/ecpC) E. coli common pilus usher EcpC [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00002	456889	457557	+	yagY/ecpB	100.0	98.1	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00002	456245	456832	+	yagZ/ecpA	100.0	98.5	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00036	10665	11624	+	ybtA	100.0	99.3	NP_405473	(ybtA) transcriptional regulator YbtA [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00027	43654	45231	-	ybtE	100.0	99.8	NP_405468	(ybtE) yersiniabactin siderophore biosynthetic protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00036	8696	10498	-	ybtP	100.0	99.6	NP_405474	(ybtP) lipoprotein inner membrane ABC-transporter [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00036	6907	8709	-	ybtQ	100.0	99.6	NP_405475	(ybtQ) inner membrane ABC-transporter YbtQ [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00036	4302	5606	-	ybtS	100.0	99.8	NP_405477	(ybtS) salicylate synthase Irp9 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00027	45235	46038	-	ybtT	100.0	99.6	NP_405469	(ybtT) yersiniabactin biosynthetic protein YbtT [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00027	46035	47135	-	ybtU	100.0	99.7	NP_405470	(ybtU) yersiniabactin biosynthetic protein YbtU [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00036	5634	6914	-	ybtX	100.0	99.7	NP_405476	(ybtX) putative signal transducer [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00002	455580	456170	+	ykgK/ecpR	100.0	99.5	NP_286011	(ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

ID013I

Contig	Start	End	Strand	Gene	Coverage	Identity	Accession	Product
contig00028	73331	73636	-	afaA	100.0	100.0	CAW30797	(afaA) fimbrial major subunit AfaA [Afimbrial adhesin AFA-I mannose-resistant adhesin (AI010)] [Escherichia coli O25b:H4 str. FV9863]
contig00028	72345	73089	-	afaB-I	100.0	99.6	CAW30798	(afaB-I) chaperone AfaB [Afimbrial adhesin AFA-I mannose-resistant adhesin (AI010)] [Escherichia coli O25b:H4 str. FV9863]
contig00028	69670	72252	-	afaC-I	100.0	99.9	CAW30799	(afaC-I) usher AfaC [Afimbrial adhesin AFA-I mannose-resistant adhesin (AI010)] [Escherichia coli O25b:H4 str. FV9863]
contig00028	69211	69654	-	afaD	100.0	100.0	CAW30800	(afaD) AfaD [Afimbrial adhesin AFA-I mannose-resistant adhesin (AI010)] [Escherichia coli O25b:H4 str. FV9863]
contig00028	67973	68458	-	afaE-I	100.0	99.6	CAW30801	(afaE-I) AFA-I adhesin [Afa/Dr family (VF0212)] [Escherichia coli O25b:H4 str. FV9863]
contig00016	71089	72517	+	aslA	100.0	98.2	AAG10151	(aslA) putative arylsulfatase [AslA (VF0238)] [Escherichia coli O18:K1:H7 str. RS218]
contig00008	172126	174072	-	chuA	100.0	99.5	NP_756170	(chuA) Outer membrane heme/hemoglobin receptor ChuA [Chu (VF0227)] [Escherichia coli CFT073]
contig00008	171049	172077	-	chuS	100.0	99.0	NP_756169	(chuS) heme oxygenase ChuS [Chu (VF0227)] [Escherichia coli CFT073]
contig00008	174714	175706	+	chuT	100.0	99.8	NP_756175	(chuT) periplasmic heme-binding protein ChuT [Chu (VF0227)] [Escherichia coli CFT073]
contig00008	178242	179234	+	chuU	100.0	99.5	NP_756179	(chuU) heme permease protein ChuU [Chu (VF0227)] [Escherichia coli CFT073]
contig00008	179201	180001	+	chuV	100.0	99.8	NP_756180	(chuV) ATP-binding hydrophilic protein ChuV [Chu (VF0227)] [Escherichia coli CFT073]
contig00008	175726	177063	+	chuW	100.0	98.9	NP_756176	(chuW) Putative oxygen independent coproporphyrinogen III oxidase [Chu (VF0227)] [Escherichia coli CFT073]
contig00008	177076	177570	+	chuX	100.0	100.0	NP_756177	(chuX) putative heme-binding protein ChuX [Chu (VF0227)] [Escherichia coli CFT073]
contig00008	177570	178193	+	chuY	100.0	98.2	NP_756178	(chuY) ChuY [Chu (VF0227)] [Escherichia coli CFT073]
contig00003	133106	133561	-	csgB	99.8	83.8	NP_460114	(csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00003	134314	134964	+	csgD	100.0	81.6	NP_460113	(csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00003	135383	135799	+	csgF	99.0	80.8	NP_460111	(csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00003	135826	136659	+	csgG	100.0	83.2	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00028	74554	74781	+	daaF	100.0	100.0	AAA23662	(daaF) DaaF protein [F1845 fimbrial adhesin (AI016)] [Escherichia coli str. C1845]
contig00028	68660	68833	-	draP	100.0	98.8	AAK16479	(draP) DraP [Dr adhesins (VF0223)] [Escherichia coli O75:K5:H- str. IH11128]
contig00001	138992	139738	-	entA	100.0	98.1	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00001	139738	140595	-	entB	100.0	99.4	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00001	142229	143416	-	entC	100.0	98.7	NP_752611	(entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00001	157905	158566	+	entD	85.9	96.7	NP_752599	(entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00001	140609	142219	-	entE	100.0	98.9	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00001	150096	153977	-	entF	100.0	98.2	NP_752604	(entF) enterobactin synthase multienzyme complex component ATP-dependent [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00001	144553	145803	-	entS	100.0	97.4	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00001	430869	435116	-	fdeC	99.9	97.4	YP_002390132	(fdeC) adhesin FdeC [FdeC (VF0506)] [Escherichia coli O45:K1:H7 str. S88]
contig00001	155640	157880	+	fepA	100.0	98.9	NP_752600	(fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00001	143593	144549	+	fepB	100.0	98.4	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00001	147904	148719	+	fepC	100.0	99.1	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00001	145902	146918	+	fepD	100.0	97.8	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00001	146915	147907	+	fepG	100.0	97.9	NP_752607	(fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00001	154195	155397	-	fes	100.0	99.0	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00030	63459	64063	-	fimA	99.8	90.8	NP_757241	(fimA) Type-1 fimbrial protein A chain precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00030	62093	62818	-	fimC	100.0	98.9	NP_757243	(fimC) Chaperone protein fimC precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00030	59390	62026	-	fimD	100.0	98.5	NP_757244	(fimD) Outer membrane usher protein fimD precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00030	64486	65082	-	fimE	100.0	98.8	NP_757240	(fimE) Type 1 fimbriae Regulatory protein fimE [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00030	58850	59383	-	fimF	100.0	96.6	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00030	58334	58837	-	fimG	100.0	98.2	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00030	57412	58323	-	fimH	100.0	97.5	NP_757248	(fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00030	62855	63394	-	fimI	100.0	98.5	NP_757242	(fimI) Fimbrin-like protein fimI precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00019	31110	33131	+	fyuA	100.0	99.8	NP_405467	(fyuA) pesticin/yersiniabactin receptor protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00006	167409	168239	+	gspC	100.0	93.9	YP_404599	(gspC) general secretion pathway protein C [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00006	168479	170329	+	gspD	100.0	96.1	YP_404600	(gspD) general secretion pathway protein D [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00006	170329	171822	+	gspE	100.0	95.0	YP_404601	(gspE) general secretion pathway protein E [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00006	171822	173021	+	gspF	100.0	94.2	YP_404602	(gspF) general secretion pathway protein F [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00006	173062	173517	+	gspG	100.0	96.0	YP_404603	(gspG) general secretion pathway protein G [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00006	173554	174084	+	gspH	100.0	94.7	YP_404604	(gspH) general secretion pathway protein H [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00006	174081	174452	+	gspI	100.0	92.2	YP_404605	(gspI) general secretion pathway protein I [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00006	174485	175054	+	gspJ	100.0	94.4	YP_404606	(gspJ) general secretion pathway protein J [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00006	175051	176028	+	gspK	100.0	96.6	YP_404607	(gspK) general secretion pathway protein K [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00006	176343	177203	+	gspL	100.0	94.8	YP_404608	(gspL) general secretion pathway protein L [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00006	177319	177740	+	gspM	99.8	92.9	YP_404609	(gspM) general secretion pathway protein M [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00019	18010	27501	+	irp1	100.0	99.8	NP_405471	(irp1) yersiniabactin biosynthetic protein Irp1 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00019	11815	17922	+	irp2	100.0	99.5	NP_405472	(irp2) yersiniabactin biosynthetic protein Irp2 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00045	8222	10003	+	iucA	100.0	99.8	NP_709454	(iucA) aerobactin synthesis protein IucA [Aerobactin (VF0123)] [Shigella flexneri 2a str. 301]
contig00045	10004	10951	+	iucB	100.0	99.8	NP_709455	(iucB) aerobactin synthesis protein IucB [Aerobactin (VF0123)] [Shigella flexneri 2a str. 301]
contig00045	10951	12693	+	iucC	100.0	98.2	NP_755500	(iucC) aerobactin siderophore biosynthesis protein IucC [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00045	12690	14011	+	iucD	98.8	96.3	NP_755499	(iucD) L-lysine 6-monooxygenase IucD [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00045	13949	16250	+	iutA	100.0	88.4	NP_755498	(iutA) ferric aerobactin receptor precusor IutA [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00006	192460	194136	-	kpsD	100.0	98.3	AAA21682	(kpsD) KpsD [K1 capsule (VF0239)] [Escherichia coli O18:K1:H7 str. RS218]
contig00006	178799	179575	+	kpsM	100.0	94.7	AAA24046	(kpsM) KpsM [K1 capsule (VF0239)] [Escherichia coli O18:K1:H7 str. RS218]
contig00003	203532	204584	+	ompA	100.0	95.8	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00045	136	449	-	papB	99.7	98.4		(papB) regulatory protein PapB [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig00045	854	1087	+	papI	100.0	94.9	NP_755468	(papI) regulatory protein PapI [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig00023	87804	88355	+	papX	100.0	97.6	NP_755457	(papX) PapX protein regulates flagellum synthesis to repress motility [P fimbriae (CVF425)] [Escherichia coli CFT073]
contig00045	17182	21081	+	sat	100.0	99.6	NP_755494	(sat) Aecreted auto transpoter toxin [Sat (VF0231)] [Escherichia coli CFT073]
contig00056	7770	8908	+	senB	99.9	99.7	YP_406304	(senB) enterotoxin [ShET2 (VF0258)] [Shigella flexneri 2a str. 301]
contig00001	450454	451207	+	yagV/ecpE	99.7	98.0	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00001	448887	450530	+	yagW/ecpD	100.0	99.2	NP_286007	(yagW/ecpD) polymerized tip adhesin of ECP fibers [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00001	446372	448897	+	yagX/ecpC	100.0	97.6	NP_286008	(yagX/ecpC) E. coli common pilus usher EcpC [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00001	445678	446346	+	yagY/ecpB	100.0	98.1	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00001	445034	445621	+	yagZ/ecpA	100.0	98.5	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00019	10665	11624	+	ybtA	100.0	99.3	NP_405473	(ybtA) transcriptional regulator YbtA [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00019	29402	30979	+	ybtE	100.0	99.8	NP_405468	(ybtE) yersiniabactin siderophore biosynthetic protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00019	8696	10498	-	ybtP	100.0	99.6	NP_405474	(ybtP) lipoprotein inner membrane ABC-transporter [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00019	6907	8709	-	ybtQ	100.0	99.6	NP_405475	(ybtQ) inner membrane ABC-transporter YbtQ [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00019	4302	5606	-	ybtS	100.0	99.8	NP_405477	(ybtS) salicylate synthase Irp9 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00019	28595	29398	+	ybtT	100.0	99.6	NP_405469	(ybtT) yersiniabactin biosynthetic protein YbtT [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00019	27498	28598	+	ybtU	100.0	99.7	NP_405470	(ybtU) yersiniabactin biosynthetic protein YbtU [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00019	5634	6914	-	ybtX	100.0	99.7	NP_405476	(ybtX) putative signal transducer [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00001	444369	444959	+	ykgK/ecpR	100.0	99.5	NP_286011	(ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

ID016I

Contig	Start	End	Strand	Gene	Coverage	Identity	Accession	Product
contig00031	25409	26837	-	aslA	100.0	93.6	AAG10151	(aslA) putative arylsulfatase [AslA (VF0238)] [Escherichia coli O18:K1:H7 str. RS218]
contig00070	14346	14840	+	chuX	100.0	82.6	NP_756177	(chuX) putative heme-binding protein ChuX [Chu (VF0227)] [Escherichia coli CFT073]
contig00033	8086	8541	+	csgB	99.8	83.8	NP_460114	(csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00378	921	1379	-	csgB	100.0	81.7	NP_460114	(csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00033	6681	7331	-	csgD	100.0	81.1	NP_460113	(csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00378	2141	2791	+	csgD	100.0	83.6	NP_460113	(csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00378	2796	3188	+	csgE	99.2	82.3	NP_460112	(csgE) curli production assembly/transport protein CsgE [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00033	5846	6262	-	csgF	99.0	81.2	NP_460111	(csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00378	3214	3596	+	csgF	91.8	80.0	NP_460111	(csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00033	4986	5819	-	csgG	100.0	83.5	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00096	60	893	+	csgG	99.8	82.7	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00056	41965	42706	-	entA	99.3	80.7	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00090	15743	16489	-	entA	100.0	95.7	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00056	42718	43575	-	entB	100.0	81.8	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00090	16489	17346	-	entB	100.0	98.1	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00090	18980	20167	-	entC	100.0	97.9	NP_752611	(entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00090	34811	35581	+	entD	100.0	95.2	NP_752599	(entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00056	43589	45199	-	entE	99.9	81.4	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00090	17360	18970	-	entE	100.0	95.5	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00090	27030	30883	-	entF	99.3	95.7	NP_752604	(entF) enterobactin synthase multienzyme complex component ATP-dependent [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00090	21490	22740	-	entS	100.0	95.4	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00245	10347	12176	+	espL1	96.3	97.7	NP_288154	(espL1) Type III secretion system effector espL1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00157	13289	15475	+	espL4	100.0	97.3	NP_290644	(espL4) Type III secretion system effector EspL4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00114	17615	18668	+	espR1	83.7	93.8	NP_287686	(espR1) Type III secretion system effector espR1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00015	3870	5004	-	espR4	99.5	84.3	NP_288396	(espR4) Type III secretion system effector espR4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00026	63384	64805	+	espX1	100.0	93.2	NP_285716	(espX1) Type III secretion system effector EspX1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00148	14865	16445	+	espX4	99.9	93.2	NP_290672	(espX4) Type III secretion system effector EspX4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00091	15315	16607	+	espX5	100.0	97.1	NP_290699	(espX5) Type III secretion system effector EspX5 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00026	24423	25234	-	espY1	99.9	87.0	NP_285753	(espY1) Type III secretion system effector EspY1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00090	32546	34786	+	fepA	100.0	96.7	NP_752600	(fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00090	20530	21486	+	fepB	100.0	97.5	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00090	24841	25656	+	fepC	100.0	97.3	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00323	4284	5071	+	fepC	96.6	80.8	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00090	22839	23855	+	fepD	100.0	96.1	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00090	23852	24844	+	fepG	100.0	94.1	NP_752607	(fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00323	3295	4287	+	fepG	100.0	80.2	NP_752607	(fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00090	31101	32303	-	fes	100.0	96.7	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00165	12990	13601	-	fimA	100.0	88.6	NP_757241	(fimA) Type-1 fimbrial protein A chain precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00165	15099	15701	-	fimB	100.0	98.2	NP_757239	(fimB) Type 1 fimbriae Regulatory protein fimB [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00165	11624	12349	-	fimC	100.0	98.9	NP_757243	(fimC) Chaperone protein fimC precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00165	8921	11557	-	fimD	100.0	98.6	NP_757244	(fimD) Outer membrane usher protein fimD precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00165	14028	14622	-	fimE	99.7	99.3	NP_757240	(fimE) Type 1 fimbriae Regulatory protein fimE [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00165	8381	8914	-	fimF	100.0	97.9	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00165	7865	8368	-	fimG	100.0	97.8	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00165	6943	7854	-	fimH	100.0	97.4	NP_757248	(fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00165	12386	12925	-	fimI	100.0	98.7	NP_757242	(fimI) Fimbrin-like protein fimI precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00013	49913	50898	-	fliG	99.3	80.2	YP_001006742	(fliG) flagellar motor switch protein G [Flagella (VF0394)] [Yersinia enterocolitica subsp. enterocolitica 8081]
contig00015	64916	66937	+	fyuA	100.0	99.9	NP_405467	(fyuA) pesticin/yersiniabactin receptor protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00118	6503	7333	+	gspC	100.0	94.7	YP_404599	(gspC) general secretion pathway protein C [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00118	7573	9423	+	gspD	100.0	96.1	YP_404600	(gspD) general secretion pathway protein D [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00118	9423	10916	+	gspE	100.0	96.9	YP_404601	(gspE) general secretion pathway protein E [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00118	10916	12115	+	gspF	100.0	96.0	YP_404602	(gspF) general secretion pathway protein F [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00118	12156	12611	+	gspG	100.0	95.0	YP_404603	(gspG) general secretion pathway protein G [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00118	12648	13177	+	gspH	99.8	94.9	YP_404604	(gspH) general secretion pathway protein H [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00118	13174	13545	+	gspI	100.0	94.9	YP_404605	(gspI) general secretion pathway protein I [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00118	13578	14147	+	gspJ	100.0	96.7	YP_404606	(gspJ) general secretion pathway protein J [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00118	14144	15121	+	gspK	100.0	97.0	YP_404607	(gspK) general secretion pathway protein K [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00118	15436	16296	+	gspL	100.0	97.0	YP_404608	(gspL) general secretion pathway protein L [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00118	16412	16834	+	gspM	100.0	98.3	YP_404609	(gspM) general secretion pathway protein M [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00015	51816	61307	+	irp1	100.0	99.3	NP_405471	(irp1) yersiniabactin biosynthetic protein Irp1 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00015	45621	51728	+	irp2	100.0	99.8	NP_405472	(irp2) yersiniabactin biosynthetic protein Irp2 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00017	33235	34275	-	ompA	100.0	98.1	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00188	3537	4595	-	ompA	99.4	86.8	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00015	44471	45430	+	ybtA	100.0	99.5	NP_405473	(ybtA) transcriptional regulator YbtA [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00015	63208	64785	+	ybtE	100.0	99.8	NP_405468	(ybtE) yersiniabactin siderophore biosynthetic protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00015	42502	44304	-	ybtP	100.0	99.6	NP_405474	(ybtP) lipoprotein inner membrane ABC-transporter [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00015	40713	42515	-	ybtQ	100.0	99.7	NP_405475	(ybtQ) inner membrane ABC-transporter YbtQ [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00015	38108	39412	-	ybtS	100.0	99.9	NP_405477	(ybtS) salicylate synthase Irp9 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00015	62401	63204	+	ybtT	100.0	99.8	NP_405469	(ybtT) yersiniabactin biosynthetic protein YbtT [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00015	61304	62404	+	ybtU	100.0	100.0	NP_405470	(ybtU) yersiniabactin biosynthetic protein YbtU [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00015	39440	40720	-	ybtX	100.0	99.7	NP_405476	(ybtX) putative signal transducer [Yersiniabactin (VF0136)] [Yersinia pestis CO92]

ID017

Contig	Start	End	Strand	Gene	Coverage	Identity	Accession	Product
contig00001	473529	473984	-	csgB	99.8	84.0	NP_460114	(csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00001	474738	475388	+	csgD	100.0	81.1	NP_460113	(csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00001	475807	476223	+	csgF	99.0	81.2	NP_460111	(csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00001	476250	477083	+	csgG	100.0	83.1	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00012	99542	100288	-	entA	100.0	96.0	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00012	100288	101145	-	entB	100.0	97.9	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00012	102779	103966	-	entC	100.0	97.5	NP_752611	(entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00012	118610	119380	+	entD	100.0	94.0	NP_752599	(entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00012	101159	102769	-	entE	100.0	95.8	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00012	110853	114682	-	entF	98.7	95.4	NP_752604	(entF) enterobactin synthase multienzyme complex component ATP-dependent [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00012	105289	106539	-	entS	100.0	95.6	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00003	74456	76324	-	espL1	98.4	95.3	NP_288154	(espL1) Type III secretion system effector espL1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00031	24866	25921	+	espR1	83.8	94.2	NP_287686	(espR1) Type III secretion system effector espR1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00007	200479	201899	+	espX1	99.9	94.7	NP_285716	(espX1) Type III secretion system effector EspX1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00011	39590	41170	+	espX4	99.9	93.1	NP_290672	(espX4) Type III secretion system effector EspX4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00011	70690	71982	-	espX5	100.0	95.7	NP_290699	(espX5) Type III secretion system effector EspX5 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00016	43044	47285	-	fdeC	99.8	92.4	YP_002390132	(fdeC) adhesin FdeC [FdeC (VF0506)] [Escherichia coli O45:K1:H7 str. S88]
contig00012	116345	118585	+	fepA	100.0	96.8	NP_752600	(fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00012	104329	105285	+	fepB	100.0	97.4	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00012	108640	109455	+	fepC	100.0	97.3	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00012	106638	107654	+	fepD	100.0	96.0	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00012	107651	108643	+	fepG	100.0	94.0	NP_752607	(fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00012	114900	116102	-	fes	100.0	96.8	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00013	97591	98196	-	fimA	100.0	92.2	NP_757241	(fimA) Type-1 fimbrial protein A chain precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00013	99695	100297	-	fimB	100.0	98.2	NP_757239	(fimB) Type 1 fimbriae Regulatory protein fimB [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00013	96225	96950	-	fimC	100.0	98.5	NP_757243	(fimC) Chaperone protein fimC precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00013	93522	96158	-	fimD	100.0	98.3	NP_757244	(fimD) Outer membrane usher protein fimD precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00013	98621	99217	-	fimE	100.0	98.7	NP_757240	(fimE) Type 1 fimbriae Regulatory protein fimE [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00013	92982	93515	-	fimF	100.0	97.4	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00013	92466	92969	-	fimG	100.0	98.0	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00013	91544	92455	-	fimH	100.0	97.3	NP_757248	(fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00013	96987	97526	-	fimI	100.0	98.3	NP_757242	(fimI) Fimbrin-like protein fimI precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00017	33893	34723	+	gspC	100.0	95.1	YP_404599	(gspC) general secretion pathway protein C [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00017	34963	36813	+	gspD	100.0	97.0	YP_404600	(gspD) general secretion pathway protein D [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00017	36813	38306	+	gspE	100.0	97.1	YP_404601	(gspE) general secretion pathway protein E [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00017	38306	39505	+	gspF	100.0	96.1	YP_404602	(gspF) general secretion pathway protein F [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00017	39546	40001	+	gspG	100.0	95.6	YP_404603	(gspG) general secretion pathway protein G [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00017	40038	40568	+	gspH	100.0	96.0	YP_404604	(gspH) general secretion pathway protein H [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00017	40565	40936	+	gspI	100.0	95.2	YP_404605	(gspI) general secretion pathway protein I [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00017	40969	41538	+	gspJ	100.0	97.2	YP_404606	(gspJ) general secretion pathway protein J [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00017	41535	42512	+	gspK	100.0	96.1	YP_404607	(gspK) general secretion pathway protein K [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00017	42827	43687	+	gspL	100.0	97.6	YP_404608	(gspL) general secretion pathway protein L [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00017	43803	44225	+	gspM	100.0	94.1	YP_404609	(gspM) general secretion pathway protein M [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	546899	547951	+	ompA	100.0	94.3	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00016	56391	57144	+	yagV/ecpE	99.7	96.8	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00016	54824	56467	+	yagW/ecpD	100.0	98.6	NP_286007	(yagW/ecpD) polymerized tip adhesin of ECP fibers [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00016	52309	54834	+	yagX/ecpC	100.0	98.7	NP_286008	(yagX/ecpC) E. coli common pilus usher EcpC [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00016	51615	52283	+	yagY/ecpB	100.0	98.7	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00016	50970	51557	+	yagZ/ecpA	100.0	99.3	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00016	50305	50895	+	ykgK/ecpR	100.0	97.6	NP_286011	(ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

ID018CT

Contig	Start	End	Strand	Gene	Coverage	Identity	Accession	Product
contig00015	49277	50705	+	aslA	100.0	93.6	AAG10151	(aslA) putative arylsulfatase [AslA (VF0238)] [Escherichia coli O18:K1:H7 str. RS218]
contig00010	100619	101074	-	csgB	99.8	83.6	NP_460114	(csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00013	422	1072	+	csgD	100.0	81.3	NP_460113	(csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00013	1491	1907	+	csgF	99.0	81.2	NP_460111	(csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00013	1934	2767	+	csgG	100.0	83.5	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00021	49253	49999	-	entA	100.0	96.0	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00021	49999	50856	-	entB	100.0	98.4	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00021	52490	53677	-	entC	100.0	97.9	NP_752611	(entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00021	68321	69091	+	entD	100.0	95.1	NP_752599	(entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00021	50870	52480	-	entE	100.0	95.6	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00021	60540	64393	-	entF	99.3	95.7	NP_752604	(entF) enterobactin synthase multienzyme complex component ATP-dependent [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00021	55000	56250	-	entS	100.0	95.4	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00054	1	1722	-	espL1	90.6	97.7	NP_288154	(espL1) Type III secretion system effector espL1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00017	74779	76200	+	espX1	100.0	95.1	NP_285716	(espX1) Type III secretion system effector EspX1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00045	13174	14466	-	espX5	100.0	96.5	NP_290699	(espX5) Type III secretion system effector EspX5 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00021	66056	68296	+	fepA	100.0	96.7	NP_752600	(fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00021	54040	54996	+	fepB	100.0	97.5	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00021	58351	59166	+	fepC	100.0	97.3	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00021	56349	57365	+	fepD	100.0	96.0	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00021	57362	58354	+	fepG	100.0	94.0	NP_752607	(fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00021	64611	65813	-	fes	100.0	96.6	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00024	59197	59801	-	fimA	99.8	90.8	NP_757241	(fimA) Type-1 fimbrial protein A chain precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00046	1110	1712	-	fimB	100.0	97.8	NP_757239	(fimB) Type 1 fimbriae Regulatory protein fimB [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00024	57831	58556	-	fimC	100.0	98.9	NP_757243	(fimC) Chaperone protein fimC precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00024	55128	57764	-	fimD	100.0	98.5	NP_757244	(fimD) Outer membrane usher protein fimD precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00046	36	632	-	fimE	100.0	98.8	NP_757240	(fimE) Type 1 fimbriae Regulatory protein fimE [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00024	54588	55121	-	fimF	100.0	97.0	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00024	54072	54575	-	fimG	100.0	97.2	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00024	53150	54061	-	fimH	100.0	97.2	NP_757248	(fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00024	58593	59132	-	fimI	100.0	98.5	NP_757242	(fimI) Fimbrin-like protein fimI precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00013	72820	73860	+	ompA	100.0	98.1	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]

ID019

Contig	Start	End	Strand	Gene	Coverage	Identity	Accession	Product
contig00018	49157	50585	+	aslA	100.0	92.9	AAG10151	(aslA) putative arylsulfatase [AslA (VF0238)] [Escherichia coli O18:K1:H7 str. RS218]
contig00006	6546	7001	+	csgB	99.8	83.6	NP_460114	(csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00006	5141	5791	-	csgD	100.0	81.3	NP_460113	(csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00006	4306	4722	-	csgF	99.0	81.2	NP_460111	(csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00006	3446	4279	-	csgG	100.0	83.5	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00011	100946	101692	-	entA	100.0	96.0	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00011	101692	102549	-	entB	100.0	98.1	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00011	104183	105370	-	entC	100.0	97.9	NP_752611	(entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00011	120014	120784	+	entD	100.0	95.2	NP_752599	(entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00011	102563	104173	-	entE	100.0	95.4	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00011	112233	116086	-	entF	99.3	95.7	NP_752604	(entF) enterobactin synthase multienzyme complex component ATP-dependent [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00011	106693	107943	-	entS	100.0	95.4	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00004	103923	105822	-	espL1	100.0	97.6	NP_288154	(espL1) Type III secretion system effector espL1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00036	25249	26303	+	espR1	83.7	93.8	NP_287686	(espR1) Type III secretion system effector espR1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00024	67116	68251	-	espR4	99.6	84.5	NP_288396	(espR4) Type III secretion system effector espR4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00001	200923	202344	+	espX1	99.9	95.3	NP_285716	(espX1) Type III secretion system effector EspX1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00014	73423	75003	-	espX4	99.9	93.2	NP_290672	(espX4) Type III secretion system effector EspX4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00014	42631	43923	+	espX5	100.0	97.0	NP_290699	(espX5) Type III secretion system effector EspX5 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00001	311902	313899	+	espX6	88.1	87.8	NP_290952	(espX6) Type III secretion system effector EspX6 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00029	391	4639	-	fdeC	99.9	94.2	YP_002390132	(fdeC) adhesin FdeC [FdeC (VF0506)] [Escherichia coli O45:K1:H7 str. S88]
contig00011	117749	119989	+	fepA	100.0	96.7	NP_752600	(fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00011	105733	106689	+	fepB	100.0	97.5	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00011	110044	110859	+	fepC	100.0	97.3	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00011	108042	109058	+	fepD	100.0	96.0	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00011	109055	110047	+	fepG	100.0	94.1	NP_752607	(fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00011	116304	117506	-	fes	100.0	96.6	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00037	22842	23446	-	fimA	99.8	92.1	NP_757241	(fimA) Type-1 fimbrial protein A chain precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00037	24943	25545	-	fimB	100.0	97.3	NP_757239	(fimB) Type 1 fimbriae Regulatory protein fimB [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00037	21476	22201	-	fimC	100.0	96.6	NP_757243	(fimC) Chaperone protein fimC precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00037	18773	21409	-	fimD	100.0	96.8	NP_757244	(fimD) Outer membrane usher protein fimD precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00037	23876	24465	-	fimE	98.8	97.1	NP_757240	(fimE) Type 1 fimbriae Regulatory protein fimE [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00037	18233	18766	-	fimF	100.0	96.6	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00037	17717	18220	-	fimG	100.0	96.4	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00037	16795	17706	-	fimH	100.0	97.7	NP_757248	(fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00037	22238	22777	-	fimI	100.0	97.6	NP_757242	(fimI) Fimbrin-like protein fimI precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00007	103875	104915	-	ompA	100.0	98.1	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00029	13745	14498	+	yagV/ecpE	99.7	97.1	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00029	12178	13821	+	yagW/ecpD	100.0	99.0	NP_286007	(yagW/ecpD) polymerized tip adhesin of ECP fibers [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00029	9663	12188	+	yagX/ecpC	100.0	98.8	NP_286008	(yagX/ecpC) E. coli common pilus usher EcpC [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00029	8969	9637	+	yagY/ecpB	100.0	98.1	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00029	8324	8911	+	yagZ/ecpA	100.0	99.2	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00029	7659	8249	+	ykgK/ecpR	100.0	96.6	NP_286011	(ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

ID01CT

Contig	Start	End	Strand	Gene	Coverage	Identity	Accession	Product
contig00032	14815	16243	+	aslA	100.0	92.9	AAG10151	(aslA) putative arylsulfatase [AslA (VF0238)] [Escherichia coli O18:K1:H7 str. RS218]
contig00012	10921	11376	+	csgB	99.8	83.6	NP_460114	(csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00012	9516	10166	-	csgD	100.0	81.3	NP_460113	(csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00012	8681	9097	-	csgF	99.0	81.2	NP_460111	(csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00012	7821	8654	-	csgG	100.0	83.5	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00003	184844	185590	-	entA	100.0	95.7	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00003	185590	186447	-	entB	100.0	98.1	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00003	188081	189268	-	entC	100.0	97.9	NP_752611	(entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00003	203912	204682	+	entD	100.0	95.2	NP_752599	(entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00003	186461	188071	-	entE	100.0	95.5	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00003	196131	199984	-	entF	99.3	95.7	NP_752604	(entF) enterobactin synthase multienzyme complex component ATP-dependent [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00003	190591	191841	-	entS	100.0	95.4	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00035	15481	17380	-	espL1	100.0	97.6	NP_288154	(espL1) Type III secretion system effector espL1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00055	11450	12504	+	espR1	83.7	94.1	NP_287686	(espR1) Type III secretion system effector espR1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00008	129464	130883	+	espX1	99.9	95.2	NP_285716	(espX1) Type III secretion system effector EspX1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00043	5629	6921	-	espX5	100.0	97.1	NP_290699	(espX5) Type III secretion system effector EspX5 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00008	90417	91198	-	espY1	99.9	90.4	NP_285753	(espY1) Type III secretion system effector EspY1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00001	254452	258700	-	fdeC	99.9	94.3	YP_002390132	(fdeC) adhesin FdeC [FdeC (VF0506)] [Escherichia coli O45:K1:H7 str. S88]
contig00003	201647	203887	+	fepA	100.0	96.7	NP_752600	(fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00003	189631	190587	+	fepB	100.0	97.5	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00003	193942	194757	+	fepC	100.0	97.3	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00003	191940	192956	+	fepD	100.0	96.1	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00003	192953	193945	+	fepG	100.0	94.1	NP_752607	(fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00003	200202	201404	-	fes	100.0	96.7	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00070	12107	12712	-	fimA	100.0	95.4	NP_757241	(fimA) Type-1 fimbrial protein A chain precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00077	6025	6627	+	fimB	100.0	98.2	NP_757239	(fimB) Type 1 fimbriae Regulatory protein fimB [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00070	10742	11467	-	fimC	100.0	99.2	NP_757243	(fimC) Chaperone protein fimC precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00070	8039	10675	-	fimD	100.0	98.9	NP_757244	(fimD) Outer membrane usher protein fimD precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00108	206	802	+	fimE	100.0	98.7	NP_757240	(fimE) Type 1 fimbriae Regulatory protein fimE [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00070	7499	8032	-	fimF	100.0	99.1	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00070	6983	7486	-	fimG	100.0	98.2	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00070	6061	6972	-	fimH	100.0	97.6	NP_757248	(fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00070	11504	12042	-	fimI	99.8	98.5	NP_757242	(fimI) Fimbrin-like protein fimI precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00019	80289	80651	+	gtrA	100.0	86.8	NP_706257	(gtrA) bactoprenol-linked glucose translocase/flippase [LPS (VF0124)] [Shigella flexneri 2a str. 301]
contig00019	80648	81552	+	gtrB	97.2	81.6	NP_706258	(gtrB) bactoprenol glucosyl transferase [LPS (VF0124)] [Shigella flexneri 2a str. 301]
contig00011	93242	94282	-	ompA	100.0	98.1	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00001	268020	268773	+	yagV/ecpE	99.7	97.1	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00001	266453	268096	+	yagW/ecpD	100.0	99.1	NP_286007	(yagW/ecpD) polymerized tip adhesin of ECP fibers [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00001	263938	266463	+	yagX/ecpC	100.0	98.8	NP_286008	(yagX/ecpC) E. coli common pilus usher EcpC [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00001	263244	263912	+	yagY/ecpB	100.0	98.1	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00001	262599	263186	+	yagZ/ecpA	100.0	99.2	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00001	261934	262524	+	ykgK/ecpR	100.0	97.0	NP_286011	(ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

ID021

Contig	Start	End	Strand	Gene	Coverage	Identity	Accession	Product
contig00019	49272	50700	+	aslA	100.0	93.6	AAG10151	(aslA) putative arylsulfatase [AslA (VF0238)] [Escherichia coli O18:K1:H7 str. RS218]
contig00018	6471	6926	+	csgB	99.8	83.8	NP_460114	(csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00018	5066	5716	-	csgD	100.0	81.1	NP_460113	(csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00018	4231	4647	-	csgF	99.0	81.2	NP_460111	(csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00018	3371	4204	-	csgG	100.0	83.5	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00016	99075	99821	-	entA	100.0	95.7	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00016	99821	100678	-	entB	100.0	98.1	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00016	102312	103499	-	entC	100.0	97.9	NP_752611	(entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00016	118143	118913	+	entD	100.0	95.2	NP_752599	(entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00016	100692	102302	-	entE	100.0	95.5	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00016	110362	114215	-	entF	99.3	95.7	NP_752604	(entF) enterobactin synthase multienzyme complex component ATP-dependent [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00016	104822	106072	-	entS	100.0	95.4	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00001	66391	68290	-	espL1	100.0	97.6	NP_288154	(espL1) Type III secretion system effector espL1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00032	37583	39769	+	espL4	100.0	97.3	NP_290644	(espL4) Type III secretion system effector EspL4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00035	25267	26320	+	espR1	83.7	93.8	NP_287686	(espR1) Type III secretion system effector espR1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00006	25291	26425	-	espR4	99.5	84.3	NP_288396	(espR4) Type III secretion system effector espR4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00005	69186	70607	-	espX1	100.0	93.2	NP_285716	(espX1) Type III secretion system effector EspX1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00032	7787	9367	-	espX4	99.9	93.2	NP_290672	(espX4) Type III secretion system effector EspX4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00031	31385	32677	+	espX5	100.0	97.1	NP_290699	(espX5) Type III secretion system effector EspX5 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00005	108757	109568	+	espY1	99.9	87.0	NP_285753	(espY1) Type III secretion system effector EspY1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00045	17762	22010	-	fdeC	99.9	94.2	YP_002390132	(fdeC) adhesin FdeC [FdeC (VF0506)] [Escherichia coli O45:K1:H7 str. S88]
contig00016	115878	118118	+	fepA	100.0	96.7	NP_752600	(fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00016	103862	104818	+	fepB	100.0	97.5	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00016	108173	108988	+	fepC	100.0	97.3	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00016	106171	107187	+	fepD	100.0	96.1	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00016	107184	108176	+	fepG	100.0	94.1	NP_752607	(fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00016	114433	115635	-	fes	100.0	96.7	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00039	25238	25849	-	fimA	100.0	88.6	NP_757241	(fimA) Type-1 fimbrial protein A chain precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00039	27347	27949	-	fimB	100.0	98.2	NP_757239	(fimB) Type 1 fimbriae Regulatory protein fimB [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00039	23872	24597	-	fimC	100.0	98.9	NP_757243	(fimC) Chaperone protein fimC precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00039	21169	23805	-	fimD	100.0	98.6	NP_757244	(fimD) Outer membrane usher protein fimD precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00039	26276	26870	-	fimE	99.7	99.3	NP_757240	(fimE) Type 1 fimbriae Regulatory protein fimE [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00039	20629	21162	-	fimF	100.0	97.9	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00039	20113	20616	-	fimG	100.0	97.8	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00039	19191	20102	-	fimH	100.0	97.4	NP_757248	(fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00039	24634	25173	-	fimI	100.0	98.7	NP_757242	(fimI) Fimbrin-like protein fimI precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00006	86337	88358	+	fyuA	100.0	99.9	NP_405467	(fyuA) pesticin/yersiniabactin receptor protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00003	122285	123115	-	gspC	100.0	94.7	YP_404599	(gspC) general secretion pathway protein C [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00003	120195	122045	-	gspD	100.0	96.1	YP_404600	(gspD) general secretion pathway protein D [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00003	118702	120195	-	gspE	100.0	96.9	YP_404601	(gspE) general secretion pathway protein E [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00003	117503	118702	-	gspF	100.0	96.0	YP_404602	(gspF) general secretion pathway protein F [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00003	117007	117462	-	gspG	100.0	95.0	YP_404603	(gspG) general secretion pathway protein G [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00003	116441	116970	-	gspH	99.8	94.9	YP_404604	(gspH) general secretion pathway protein H [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00003	116073	116444	-	gspI	100.0	94.9	YP_404605	(gspI) general secretion pathway protein I [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00003	115471	116040	-	gspJ	100.0	96.7	YP_404606	(gspJ) general secretion pathway protein J [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00003	114497	115474	-	gspK	100.0	97.0	YP_404607	(gspK) general secretion pathway protein K [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00003	113322	114182	-	gspL	100.0	97.0	YP_404608	(gspL) general secretion pathway protein L [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00003	112784	113206	-	gspM	100.0	98.3	YP_404609	(gspM) general secretion pathway protein M [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00006	73237	82728	+	irp1	100.0	99.3	NP_405471	(irp1) yersiniabactin biosynthetic protein Irp1 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00006	67042	73149	+	irp2	100.0	99.8	NP_405472	(irp2) yersiniabactin biosynthetic protein Irp2 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00004	145353	146393	-	ompA	100.0	98.1	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00006	65892	66851	+	ybtA	100.0	99.5	NP_405473	(ybtA) transcriptional regulator YbtA [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00006	84629	86206	+	ybtE	100.0	99.8	NP_405468	(ybtE) yersiniabactin siderophore biosynthetic protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00006	63923	65725	-	ybtP	100.0	99.6	NP_405474	(ybtP) lipoprotein inner membrane ABC-transporter [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00006	62134	63936	-	ybtQ	100.0	99.7	NP_405475	(ybtQ) inner membrane ABC-transporter YbtQ [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00006	59529	60833	-	ybtS	100.0	99.9	NP_405477	(ybtS) salicylate synthase Irp9 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00006	83822	84625	+	ybtT	100.0	99.8	NP_405469	(ybtT) yersiniabactin biosynthetic protein YbtT [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00006	82725	83825	+	ybtU	100.0	100.0	NP_405470	(ybtU) yersiniabactin biosynthetic protein YbtU [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00006	60861	62141	-	ybtX	100.0	99.7	NP_405476	(ybtX) putative signal transducer [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00045	25032	25622	+	ykgK/ecpR	100.0	97.0	NP_286011	(ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

ID027

Contig	Start	End	Strand	Gene	Coverage	Identity	Accession	Product
contig00002	55091	55279	+	afaF-VII	100.0	98.4	AAK16195	(afaF-VII) AfaF-VII [Afimbrial adhesin AfaE-VIII (AI015)] [Escherichia coli str. 239 KH 89]
contig00024	49071	50499	+	aslA	100.0	93.6	AAG10151	(aslA) putative arylsulfatase [AslA (VF0238)] [Escherichia coli O18:K1:H7 str. RS218]
contig00019	97680	97796	-	astA	100.0	95.7	BAA94855	(astA) heat-stable enterotoxin 1 [EAST1 (VF0216)] [Escherichia coli O44:H18 042]
contig00090	767	883	+	astA	100.0	100.0	BAA94855	(astA) heat-stable enterotoxin 1 [EAST1 (VF0216)] [Escherichia coli O44:H18 042]
contig00016	8085	8540	+	csgB	99.8	83.6	NP_460114	(csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00016	6680	7330	-	csgD	100.0	81.1	NP_460113	(csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00016	5845	6261	-	csgF	99.0	81.2	NP_460111	(csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00016	4985	5818	-	csgG	100.0	83.5	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00015	99305	100051	-	entA	100.0	95.7	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00015	100051	100908	-	entB	100.0	98.1	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00015	102542	103729	-	entC	100.0	97.9	NP_752611	(entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00015	118373	119143	+	entD	100.0	95.2	NP_752599	(entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00015	100922	102532	-	entE	100.0	95.5	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00015	110592	114445	-	entF	99.3	95.7	NP_752604	(entF) enterobactin synthase multienzyme complex component ATP-dependent [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00015	105052	106302	-	entS	100.0	95.4	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00005	75100	76999	-	espL1	100.0	97.4	NP_288154	(espL1) Type III secretion system effector espL1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00013	120641	122827	+	espL4	100.0	97.3	NP_290644	(espL4) Type III secretion system effector EspL4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00041	25250	26304	+	espR1	83.7	94.0	NP_287686	(espR1) Type III secretion system effector espR1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00004	203533	204954	+	espX1	100.0	95.8	NP_285716	(espX1) Type III secretion system effector EspX1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00013	90845	92425	-	espX4	99.9	93.4	NP_290672	(espX4) Type III secretion system effector EspX4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00013	60054	61346	+	espX5	100.0	97.1	NP_290699	(espX5) Type III secretion system effector EspX5 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00004	164471	165267	-	espY1	99.9	88.7	NP_285753	(espY1) Type III secretion system effector EspY1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00003	204591	208839	-	fdeC	99.9	94.2	YP_002390132	(fdeC) adhesin FdeC [FdeC (VF0506)] [Escherichia coli O45:K1:H7 str. S88]
contig00015	116108	118348	+	fepA	100.0	96.7	NP_752600	(fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00015	104092	105048	+	fepB	100.0	97.5	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00015	108403	109218	+	fepC	100.0	97.3	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00015	106401	107417	+	fepD	100.0	96.1	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00015	107414	108406	+	fepG	100.0	94.1	NP_752607	(fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00015	114663	115865	-	fes	100.0	96.7	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00048	11895	12499	-	fimA	99.8	90.8	NP_757241	(fimA) Type-1 fimbrial protein A chain precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00048	13997	14599	-	fimB	100.0	97.8	NP_757239	(fimB) Type 1 fimbriae Regulatory protein fimB [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00048	10529	11254	-	fimC	100.0	98.6	NP_757243	(fimC) Chaperone protein fimC precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00048	7826	10462	-	fimD	100.0	98.9	NP_757244	(fimD) Outer membrane usher protein fimD precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00048	12923	13519	-	fimE	100.0	98.8	NP_757240	(fimE) Type 1 fimbriae Regulatory protein fimE [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00048	7286	7819	-	fimF	100.0	99.1	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00048	6770	7273	-	fimG	100.0	98.4	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00048	5848	6759	-	fimH	100.0	97.5	NP_757248	(fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00048	11291	11830	-	fimI	100.0	98.5	NP_757242	(fimI) Fimbrin-like protein fimI precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00029	42042	44063	+	fyuA	100.0	99.9	NP_405467	(fyuA) pesticin/yersiniabactin receptor protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00002	82007	82837	-	gspC	100.0	94.7	YP_404599	(gspC) general secretion pathway protein C [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00002	79917	81767	-	gspD	100.0	96.1	YP_404600	(gspD) general secretion pathway protein D [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00002	78424	79917	-	gspE	100.0	97.0	YP_404601	(gspE) general secretion pathway protein E [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00002	77225	78424	-	gspF	100.0	96.0	YP_404602	(gspF) general secretion pathway protein F [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00002	76729	77184	-	gspG	100.0	95.0	YP_404603	(gspG) general secretion pathway protein G [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00002	76162	76692	-	gspH	100.0	95.5	YP_404604	(gspH) general secretion pathway protein H [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00002	75794	76165	-	gspI	100.0	95.2	YP_404605	(gspI) general secretion pathway protein I [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00002	75192	75761	-	gspJ	100.0	96.7	YP_404606	(gspJ) general secretion pathway protein J [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00002	74218	75195	-	gspK	100.0	97.0	YP_404607	(gspK) general secretion pathway protein K [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00002	73043	73903	-	gspL	100.0	97.1	YP_404608	(gspL) general secretion pathway protein L [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00002	72505	72927	-	gspM	100.0	98.3	YP_404609	(gspM) general secretion pathway protein M [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00029	28942	38433	+	irp1	100.0	99.7	NP_405471	(irp1) yersiniabactin biosynthetic protein Irp1 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00029	22747	28854	+	irp2	100.0	99.7	NP_405472	(irp2) yersiniabactin biosynthetic protein Irp2 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00050	7016	8803	+	iucA	100.0	94.2	NP_755502	(iucA) aerobactin siderophore biosynthesis protein IucD [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00050	8804	9751	+	iucB	100.0	95.6	NP_755501	(iucB) aerobactin siderophore biosynthesis protein IucB [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00050	9751	11493	+	iucC	100.0	96.0	NP_755500	(iucC) aerobactin siderophore biosynthesis protein IucC [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00050	11490	12811	+	iucD	98.8	96.3	NP_755499	(iucD) L-lysine 6-monooxygenase IucD [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00050	12749	15050	+	iutA	100.0	88.4	NP_755498	(iutA) ferric aerobactin receptor precusor IutA [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00035	21025	22065	-	ompA	100.0	98.1	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00003	217946	218699	+	yagV/ecpE	99.7	97.0	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00003	216379	218022	+	yagW/ecpD	100.0	99.0	NP_286007	(yagW/ecpD) polymerized tip adhesin of ECP fibers [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00003	213864	216389	+	yagX/ecpC	100.0	98.8	NP_286008	(yagX/ecpC) E. coli common pilus usher EcpC [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00003	213170	213838	+	yagY/ecpB	100.0	98.1	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00003	212525	213112	+	yagZ/ecpA	100.0	99.2	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00029	21597	22556	+	ybtA	100.0	99.6	NP_405473	(ybtA) transcriptional regulator YbtA [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00029	40334	41911	+	ybtE	100.0	99.9	NP_405468	(ybtE) yersiniabactin siderophore biosynthetic protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00029	19628	21430	-	ybtP	100.0	99.5	NP_405474	(ybtP) lipoprotein inner membrane ABC-transporter [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00029	17839	19641	-	ybtQ	100.0	99.7	NP_405475	(ybtQ) inner membrane ABC-transporter YbtQ [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00029	15234	16538	-	ybtS	100.0	99.7	NP_405477	(ybtS) salicylate synthase Irp9 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00029	39527	40330	+	ybtT	100.0	99.9	NP_405469	(ybtT) yersiniabactin biosynthetic protein YbtT [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00029	38430	39530	+	ybtU	100.0	99.8	NP_405470	(ybtU) yersiniabactin biosynthetic protein YbtU [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00029	16566	17846	-	ybtX	100.0	99.5	NP_405476	(ybtX) putative signal transducer [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00003	211860	212450	+	ykgK/ecpR	100.0	97.0	NP_286011	(ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

ID031

Contig	Start	End	Strand	Gene	Coverage	Identity	Accession	Product
contig00135	1568	1873	-	afaA	100.0	99.7	CAW30797	(afaA) fimbrial major subunit AfaA [Afimbrial adhesin AFA-I mannose-resistant adhesin (AI010)] [Escherichia coli O25b:H4 str. FV9863]
contig00136	1552	1857	-	afaA	100.0	100.0	CAW30797	(afaA) fimbrial major subunit AfaA [Afimbrial adhesin AFA-I mannose-resistant adhesin (AI010)] [Escherichia coli O25b:H4 str. FV9863]
contig00135	554	1298	-	afaB-I	100.0	99.6	CAW30798	(afaB-I) chaperone AfaB [Afimbrial adhesin AFA-I mannose-resistant adhesin (AI010)] [Escherichia coli O25b:H4 str. FV9863]
contig00136	554	1298	-	afaB-I	100.0	99.1	CAW30798	(afaB-I) chaperone AfaB [Afimbrial adhesin AFA-I mannose-resistant adhesin (AI010)] [Escherichia coli O25b:H4 str. FV9863]
contig00091	7237	7680	-	afaD	100.0	94.4	CAW30800	(afaD) AfaD [Afimbrial adhesin AFA-I mannose-resistant adhesin (AI010)] [Escherichia coli O25b:H4 str. FV9863]
contig00027	16578	18006	+	aslA	100.0	92.9	AAG10151	(aslA) putative arylsulfatase [AslA (VF0238)] [Escherichia coli O18:K1:H7 str. RS218]
contig00008	93711	94166	-	csgB	99.8	83.6	NP_460114	(csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00008	94921	95571	+	csgD	100.0	81.3	NP_460113	(csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00008	95990	96406	+	csgF	99.0	81.2	NP_460111	(csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00008	96433	97266	+	csgG	100.0	83.5	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00087	2131	2358	+	daaF	100.0	100.0	AAA23662	(daaF) DaaF protein [F1845 fimbrial adhesin (AI016)] [Escherichia coli str. C1845]
contig00152	383	610	+	daaF	100.0	98.7	AAA23662	(daaF) DaaF protein [F1845 fimbrial adhesin (AI016)] [Escherichia coli str. C1845]
contig00008	118802	119245	-	draD	100.0	100.0	AAK16478	(draD) DraD periplasmic protein [Dr adhesins (VF0223)] [Escherichia coli O75:K5:H- str. IH11128]
contig00008	118250	118423	-	draP	100.0	100.0	AAK16479	(draP) DraP [Dr adhesins (VF0223)] [Escherichia coli O75:K5:H- str. IH11128]
contig00091	6656	6829	-	draP	100.0	98.8	AAK16479	(draP) DraP [Dr adhesins (VF0223)] [Escherichia coli O75:K5:H- str. IH11128]
contig00021	53688	54434	-	entA	100.0	95.7	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00021	54434	55291	-	entB	100.0	98.1	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00021	56925	58112	-	entC	100.0	97.9	NP_752611	(entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00021	72756	73526	+	entD	100.0	95.2	NP_752599	(entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00021	55305	56915	-	entE	100.0	95.4	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00021	64975	68828	-	entF	99.3	95.7	NP_752604	(entF) enterobactin synthase multienzyme complex component ATP-dependent [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00021	59435	60685	-	entS	100.0	95.4	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00024	7950	9849	-	espL1	100.0	97.6	NP_288154	(espL1) Type III secretion system effector espL1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00034	28677	30257	+	espX4	100.0	96.5	NP_290672	(espX4) Type III secretion system effector EspX4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00043	23183	24475	+	espX5	100.0	97.1	NP_290699	(espX5) Type III secretion system effector EspX5 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00006	90777	91410	-	espY1	84.2	92.9	NP_285753	(espY1) Type III secretion system effector EspY1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00029	46313	50561	-	fdeC	99.9	94.2	YP_002390132	(fdeC) adhesin FdeC [FdeC (VF0506)] [Escherichia coli O45:K1:H7 str. S88]
contig00021	70491	72731	+	fepA	100.0	96.7	NP_752600	(fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00021	58475	59431	+	fepB	100.0	97.5	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00021	62786	63601	+	fepC	100.0	97.3	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00021	60784	61800	+	fepD	100.0	96.1	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00021	61797	62789	+	fepG	100.0	94.1	NP_752607	(fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00021	69046	70248	-	fes	100.0	96.7	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00055	7903	9924	+	fyuA	100.0	99.9	NP_405467	(fyuA) pesticin/yersiniabactin receptor protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00033	5111	11218	-	irp2	100.0	99.5	NP_405472	(irp2) yersiniabactin biosynthetic protein Irp2 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00065	7462	9249	+	iucA	100.0	94.3	NP_755502	(iucA) aerobactin siderophore biosynthesis protein IucD [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00065	9250	10197	+	iucB	100.0	95.8	NP_755501	(iucB) aerobactin siderophore biosynthesis protein IucB [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00065	10197	11939	+	iucC	100.0	96.2	NP_755500	(iucC) aerobactin siderophore biosynthesis protein IucC [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00065	11936	13257	+	iucD	98.8	96.3	NP_755499	(iucD) L-lysine 6-monooxygenase IucD [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00065	13195	15496	+	iutA	100.0	88.4	NP_755498	(iutA) ferric aerobactin receptor precusor IutA [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00032	16892	17932	-	ompA	100.0	98.0	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00137	441	754	-	papB	99.7	98.4		(papB) regulatory protein PapB [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig00160	21	560	+	papE	99.4	93.9	NP_755460	(papE) P pilus minor subunit PapE [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig00137	1159	1392	+	papI	100.0	95.3	NP_755468	(papI) regulatory protein PapI [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig00128	2675	3226	+	papX	100.0	97.6	NP_755457	(papX) PapX protein regulates flagellum synthesis to repress motility [P fimbriae (CVF425)] [Escherichia coli CFT073]
contig00065	16429	20328	+	sat	100.0	99.5	NP_755494	(sat) Aecreted auto transpoter toxin [Sat (VF0231)] [Escherichia coli CFT073]
contig00031	6127	6880	+	yagV/ecpE	99.7	97.1	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00031	4560	6203	+	yagW/ecpD	100.0	99.1	NP_286007	(yagW/ecpD) polymerized tip adhesin of ECP fibers [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00031	2045	4570	+	yagX/ecpC	100.0	98.8	NP_286008	(yagX/ecpC) E. coli common pilus usher EcpC [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00031	1351	2019	+	yagY/ecpB	100.0	97.9	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00031	706	1293	+	yagZ/ecpA	100.0	99.2	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00033	11409	12368	-	ybtA	100.0	99.5	NP_405473	(ybtA) transcriptional regulator YbtA [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00055	6194	7771	+	ybtE	100.0	99.8	NP_405468	(ybtE) yersiniabactin siderophore biosynthetic protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00033	12535	14337	+	ybtP	100.0	99.7	NP_405474	(ybtP) lipoprotein inner membrane ABC-transporter [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00033	14324	16126	+	ybtQ	100.0	99.7	NP_405475	(ybtQ) inner membrane ABC-transporter YbtQ [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00033	17427	18731	+	ybtS	100.0	99.6	NP_405477	(ybtS) salicylate synthase Irp9 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00055	5387	6190	+	ybtT	100.0	99.6	NP_405469	(ybtT) yersiniabactin biosynthetic protein YbtT [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00055	4290	5390	+	ybtU	100.0	99.5	NP_405470	(ybtU) yersiniabactin biosynthetic protein YbtU [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00033	16119	17399	+	ybtX	100.0	99.8	NP_405476	(ybtX) putative signal transducer [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00031	41	631	+	ykgK/ecpR	100.0	96.8	NP_286011	(ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

ID034I

Contig	Start	End	Strand	Gene	Coverage	Identity	Accession	Product
contig00022	49065	50493	+	aslA	100.0	93.6	AAG10151	(aslA) putative arylsulfatase [AslA (VF0238)] [Escherichia coli O18:K1:H7 str. RS218]
contig00007	8267	8722	+	csgB	99.8	83.8	NP_460114	(csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00007	6862	7512	-	csgD	100.0	81.1	NP_460113	(csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00007	6027	6443	-	csgF	99.0	81.2	NP_460111	(csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00007	5167	6000	-	csgG	100.0	83.5	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00016	99076	99822	-	entA	100.0	95.7	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00016	99822	100679	-	entB	100.0	98.1	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00016	102313	103500	-	entC	100.0	97.9	NP_752611	(entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00016	118144	118914	+	entD	100.0	95.2	NP_752599	(entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00016	100693	102303	-	entE	100.0	95.4	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00016	110363	114216	-	entF	99.3	95.7	NP_752604	(entF) enterobactin synthase multienzyme complex component ATP-dependent [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00016	104823	106073	-	entS	100.0	95.4	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00001	295113	297012	-	espL1	100.0	97.6	NP_288154	(espL1) Type III secretion system effector espL1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00005	7233	9419	-	espL4	100.0	97.3	NP_290644	(espL4) Type III secretion system effector EspL4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00034	25267	26320	+	espR1	83.7	93.8	NP_287686	(espR1) Type III secretion system effector espR1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00001	54129	55264	+	espR4	99.6	84.5	NP_288396	(espR4) Type III secretion system effector espR4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00008	144216	145637	+	espX1	100.0	93.2	NP_285716	(espX1) Type III secretion system effector EspX1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00005	37635	39215	+	espX4	99.9	93.3	NP_290672	(espX4) Type III secretion system effector EspX4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00005	68714	70006	-	espX5	100.0	97.1	NP_290699	(espX5) Type III secretion system effector EspX5 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00008	105289	106070	-	espY1	99.9	90.4	NP_285753	(espY1) Type III secretion system effector EspY1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00003	204827	209075	-	fdeC	99.9	94.2	YP_002390132	(fdeC) adhesin FdeC [FdeC (VF0506)] [Escherichia coli O45:K1:H7 str. S88]
contig00016	115879	118119	+	fepA	100.0	96.7	NP_752600	(fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00016	103863	104819	+	fepB	100.0	97.5	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00016	108174	108989	+	fepC	100.0	97.3	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00016	106172	107188	+	fepD	100.0	96.1	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00016	107185	108177	+	fepG	100.0	94.1	NP_752607	(fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00016	114434	115636	-	fes	100.0	96.7	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00038	34579	35190	-	fimA	100.0	88.4	NP_757241	(fimA) Type-1 fimbrial protein A chain precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00050	1423	2025	-	fimB	100.0	98.2	NP_757239	(fimB) Type 1 fimbriae Regulatory protein fimB [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00038	33213	33938	-	fimC	100.0	98.9	NP_757243	(fimC) Chaperone protein fimC precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00038	30510	33146	-	fimD	100.0	98.6	NP_757244	(fimD) Outer membrane usher protein fimD precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00050	352	946	-	fimE	99.7	99.3	NP_757240	(fimE) Type 1 fimbriae Regulatory protein fimE [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00038	29970	30503	-	fimF	100.0	97.9	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00038	29454	29957	-	fimG	100.0	97.8	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00038	28532	29443	-	fimH	100.0	97.4	NP_757248	(fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00038	33975	34514	-	fimI	100.0	98.7	NP_757242	(fimI) Fimbrin-like protein fimI precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00006	103766	104806	-	ompA	100.0	98.0	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00003	218183	218936	+	yagV/ecpE	99.7	97.1	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00003	216616	218259	+	yagW/ecpD	100.0	99.1	NP_286007	(yagW/ecpD) polymerized tip adhesin of ECP fibers [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00003	214101	216626	+	yagX/ecpC	100.0	98.8	NP_286008	(yagX/ecpC) E. coli common pilus usher EcpC [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00003	213407	214075	+	yagY/ecpB	100.0	98.1	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00003	212762	213349	+	yagZ/ecpA	100.0	99.2	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00003	212097	212687	+	ykgK/ecpR	100.0	97.0	NP_286011	(ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

ID041

Contig	Start	End	Strand	Gene	Coverage	Identity	Accession	Product
contig00040	19968	20318	+	aap/aspU	100.0	96.6	YP_006099176	(aap/aspU) Dispersin [Dispersin (VF0215)] [Escherichia coli O44:H18 042]
contig00024	51586	53014	+	aslA	100.0	96.8	AAG10151	(aslA) putative arylsulfatase [AslA (VF0238)] [Escherichia coli O18:K1:H7 str. RS218]
contig00040	20752	20868	-	astA	100.0	96.6	BAA94855	(astA) heat-stable enterotoxin 1 [EAST1 (VF0216)] [Escherichia coli O44:H18 042]
contig00050	5097	5213	+	astA	100.0	98.3	BAA94855	(astA) heat-stable enterotoxin 1 [EAST1 (VF0216)] [Escherichia coli O44:H18 042]
contig00014	61352	62380	+	chuS	100.0	96.4	NP_756169	(chuS) heme oxygenase ChuS [Chu (VF0227)] [Escherichia coli CFT073]
contig00014	54196	55188	-	chuU	100.0	96.3	NP_756179	(chuU) heme permease protein ChuU [Chu (VF0227)] [Escherichia coli CFT073]
contig00014	53429	54229	-	chuV	100.0	98.4	NP_756180	(chuV) ATP-binding hydrophilic protein ChuV [Chu (VF0227)] [Escherichia coli CFT073]
contig00014	56367	57704	-	chuW	100.0	96.6	NP_756176	(chuW) Putative oxygen independent coproporphyrinogen III oxidase [Chu (VF0227)] [Escherichia coli CFT073]
contig00014	55237	55860	-	chuY	100.0	96.8	NP_756178	(chuY) ChuY [Chu (VF0227)] [Escherichia coli CFT073]
contig00012	123498	123953	-	csgB	99.8	83.4	NP_460114	(csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00012	124708	125358	+	csgD	100.0	81.4	NP_460113	(csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00012	125777	126193	+	csgF	99.0	81.0	NP_460111	(csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00012	126220	127053	+	csgG	100.0	83.0	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00011	84772	85518	-	entA	100.0	95.7	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00011	85518	86375	-	entB	100.0	98.4	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00011	88009	89196	-	entC	100.0	97.2	NP_752611	(entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00011	103654	104424	+	entD	100.0	93.9	NP_752599	(entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00011	86389	87999	-	entE	100.0	96.4	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00011	95873	99726	-	entF	99.3	95.4	NP_752604	(entF) enterobactin synthase multienzyme complex component ATP-dependent [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00011	90333	91583	-	entS	100.0	96.2	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00002	252538	254436	-	espL1	100.0	96.7	NP_288154	(espL1) Type III secretion system effector espL1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00019	87664	89850	+	espL4	100.0	96.5	NP_290644	(espL4) Type III secretion system effector EspL4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00009	14559	15811	-	espR1	99.4	93.9	NP_287686	(espR1) Type III secretion system effector espR1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00004	201632	203053	+	espX1	100.0	96.1	NP_285716	(espX1) Type III secretion system effector EspX1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00018	89264	91276	-	espX2	100.0	96.5	NP_286562	(espX2) Type III secretion system effector EspX2 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00019	53905	55485	-	espX4	100.0	96.0	NP_290672	(espX4) Type III secretion system effector EspX4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00019	23110	24402	+	espX5	100.0	96.1	NP_290699	(espX5) Type III secretion system effector EspX5 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00004	162205	162933	-	espY1	96.8	93.3	NP_285753	(espY1) Type III secretion system effector EspY1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00004	145158	145727	-	espY2	100.0	93.9	NP_285765	(espY2) Type III secretion system effector EspY2 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00013	5678	7249	-	espY3	100.0	95.8	NP_286160	(espY3) Type III secretion system effector EspY3 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00003	184296	186704	-	espY4	100.0	93.0	NP_290352	(espY4) Type III secretion system effector EspY4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00008	96670	100920	-	fdeC	100.0	95.2	YP_002390132	(fdeC) adhesin FdeC [FdeC (VF0506)] [Escherichia coli O45:K1:H7 str. S88]
contig00011	101389	103629	+	fepA	100.0	97.1	NP_752600	(fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00011	89373	90329	+	fepB	100.0	97.1	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00011	93684	94499	+	fepC	100.0	96.8	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00011	91682	92698	+	fepD	100.0	96.7	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00011	92695	93687	+	fepG	100.0	94.1	NP_752607	(fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00011	99944	101146	-	fes	100.0	96.4	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00010	122297	122902	-	fimA	100.0	90.9	NP_757241	(fimA) Type-1 fimbrial protein A chain precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00010	124400	125003	-	fimB	100.0	97.5	NP_757239	(fimB) Type 1 fimbriae Regulatory protein fimB [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00010	120931	121656	-	fimC	100.0	98.6	NP_757243	(fimC) Chaperone protein fimC precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00010	118228	120864	-	fimD	100.0	98.6	NP_757244	(fimD) Outer membrane usher protein fimD precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00010	123326	123922	-	fimE	100.0	98.8	NP_757240	(fimE) Type 1 fimbriae Regulatory protein fimE [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00010	117688	118221	-	fimF	100.0	97.6	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00010	117172	117675	-	fimG	100.0	99.0	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00010	116250	117161	-	fimH	100.0	97.7	NP_757248	(fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00010	121693	122232	-	fimI	100.0	98.3	NP_757242	(fimI) Fimbrin-like protein fimI precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00001	57571	58401	+	gspC	100.0	95.4	YP_404599	(gspC) general secretion pathway protein C [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	58641	60491	+	gspD	100.0	96.7	YP_404600	(gspD) general secretion pathway protein D [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	60491	61984	+	gspE	100.0	95.5	YP_404601	(gspE) general secretion pathway protein E [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	61984	63183	+	gspF	100.0	94.7	YP_404602	(gspF) general secretion pathway protein F [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	63224	63679	+	gspG	100.0	96.7	YP_404603	(gspG) general secretion pathway protein G [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	63716	64246	+	gspH	100.0	96.2	YP_404604	(gspH) general secretion pathway protein H [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	64243	64614	+	gspI	100.0	94.9	YP_404605	(gspI) general secretion pathway protein I [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	64647	65216	+	gspJ	100.0	94.6	YP_404606	(gspJ) general secretion pathway protein J [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	65213	66190	+	gspK	100.0	97.1	YP_404607	(gspK) general secretion pathway protein K [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	66505	67365	+	gspL	100.0	95.8	YP_404608	(gspL) general secretion pathway protein L [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	67481	67902	+	gspM	99.8	97.6	YP_404609	(gspM) general secretion pathway protein M [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	81054	82730	-	kpsD	100.0	99.3	AAA21682	(kpsD) KpsD [K1 capsule (VF0239)] [Escherichia coli O18:K1:H7 str. RS218]
contig00001	68960	69736	+	kpsM	100.0	99.9	AAA24046	(kpsM) KpsM [K1 capsule (VF0239)] [Escherichia coli O18:K1:H7 str. RS218]
contig00001	69733	70392	+	kpsT	100.0	100.0	AAA24047	(kpsT) KpsT [K1 capsule (VF0239)] [Escherichia coli O18:K1:H7 str. RS218]
contig00023	58746	59798	-	ompA	100.0	95.7	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00014	59321	61303	+	shuA	100.0	98.6	YP_405019	(shuA) outer membrane heme/hemoglobin receptor ShuA [Shu (VF0256)] [Shigella dysenteriae Sd197]
contig00014	57724	58716	-	shuT	100.0	98.0	YP_405017	(shuT) periplasmic binding protein ShuT [Shu (VF0256)] [Shigella dysenteriae Sd197]
contig00014	55860	56354	-	shuX	100.0	96.2	YP_405016	(shuX) shu locus protein ShuX [Shu (VF0256)] [Shigella dysenteriae Sd197]
contig00008	116324	117077	+	yagV/ecpE	99.7	97.1	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00008	114757	116400	+	yagW/ecpD	100.0	99.1	NP_286007	(yagW/ecpD) polymerized tip adhesin of ECP fibers [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00008	112242	114767	+	yagX/ecpC	100.0	98.0	NP_286008	(yagX/ecpC) E. coli common pilus usher EcpC [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00008	111548	112216	+	yagY/ecpB	100.0	98.5	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00008	110904	111491	+	yagZ/ecpA	100.0	99.0	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00008	110239	110829	+	ykgK/ecpR	100.0	99.0	NP_286011	(ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

ID043I

Contig	Start	End	Strand	Gene	Coverage	Identity	Accession	Product
contig00016	49279	50707	+	aslA	100.0	93.6	AAG10151	(aslA) putative arylsulfatase [AslA (VF0238)] [Escherichia coli O18:K1:H7 str. RS218]
contig00032	8086	8541	+	csgB	99.8	83.8	NP_460114	(csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00032	6681	7331	-	csgD	100.0	81.1	NP_460113	(csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00032	5846	6262	-	csgF	99.0	81.2	NP_460111	(csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00032	4986	5819	-	csgG	100.0	83.5	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00023	48009	48755	-	entA	100.0	95.7	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00023	48755	49612	-	entB	100.0	98.0	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00023	51246	52433	-	entC	100.0	97.9	NP_752611	(entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00023	67077	67847	+	entD	100.0	95.2	NP_752599	(entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00023	49626	51236	-	entE	100.0	95.5	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00023	59296	63149	-	entF	99.3	95.7	NP_752604	(entF) enterobactin synthase multienzyme complex component ATP-dependent [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00023	53756	55006	-	entS	100.0	95.4	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00004	19954	21853	-	espL1	100.0	97.5	NP_288154	(espL1) Type III secretion system effector espL1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00051	19363	21549	+	espL4	100.0	97.3	NP_290644	(espL4) Type III secretion system effector EspL4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00042	25445	26498	+	espR1	83.7	93.8	NP_287686	(espR1) Type III secretion system effector espR1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00003	203174	204595	+	espX1	100.0	95.2	NP_285716	(espX1) Type III secretion system effector EspX1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00041	8865	10445	+	espX4	99.9	93.3	NP_290672	(espX4) Type III secretion system effector EspX4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00003	164219	165030	-	espY1	99.9	87.0	NP_285753	(espY1) Type III secretion system effector EspY1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00002	204931	209179	-	fdeC	99.9	94.2	YP_002390132	(fdeC) adhesin FdeC [FdeC (VF0506)] [Escherichia coli O45:K1:H7 str. S88]
contig00023	64812	67052	+	fepA	100.0	96.7	NP_752600	(fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00023	52796	53752	+	fepB	100.0	97.5	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00023	57107	57922	+	fepC	100.0	97.3	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00023	55105	56121	+	fepD	100.0	96.1	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00023	56118	57110	+	fepG	100.0	94.1	NP_752607	(fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00023	63367	64569	-	fes	100.0	96.7	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00044	28795	29400	-	fimA	100.0	92.6	NP_757241	(fimA) Type-1 fimbrial protein A chain precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00044	30899	31501	-	fimB	100.0	98.2	NP_757239	(fimB) Type 1 fimbriae Regulatory protein fimB [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00044	27429	28154	-	fimC	100.0	98.5	NP_757243	(fimC) Chaperone protein fimC precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00044	24726	27362	-	fimD	100.0	98.3	NP_757244	(fimD) Outer membrane usher protein fimD precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00044	29825	30421	-	fimE	100.0	98.7	NP_757240	(fimE) Type 1 fimbriae Regulatory protein fimE [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00044	24186	24719	-	fimF	100.0	97.4	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00044	23670	24173	-	fimG	100.0	97.8	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00044	22748	23659	-	fimH	100.0	97.3	NP_757248	(fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00044	28191	28730	-	fimI	100.0	98.3	NP_757242	(fimI) Fimbrin-like protein fimI precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00020	41806	43827	+	fyuA	100.0	99.8	NP_405467	(fyuA) pesticin/yersiniabactin receptor protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00020	28706	38197	+	irp1	100.0	99.8	NP_405471	(irp1) yersiniabactin biosynthetic protein Irp1 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00020	22511	28618	+	irp2	100.0	99.8	NP_405472	(irp2) yersiniabactin biosynthetic protein Irp2 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00065	7017	8804	+	iucA	100.0	94.2	NP_755502	(iucA) aerobactin siderophore biosynthesis protein IucD [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00065	8805	9752	+	iucB	100.0	95.6	NP_755501	(iucB) aerobactin siderophore biosynthesis protein IucB [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00065	9752	11494	+	iucC	100.0	96.0	NP_755500	(iucC) aerobactin siderophore biosynthesis protein IucC [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00065	11491	12812	+	iucD	98.8	96.3	NP_755499	(iucD) L-lysine 6-monooxygenase IucD [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00065	12750	15051	+	iutA	100.0	88.4	NP_755498	(iutA) ferric aerobactin receptor precusor IutA [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00007	103863	104903	-	ompA	100.0	98.1	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00002	218286	219039	+	yagV/ecpE	99.7	97.1	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00002	216719	218362	+	yagW/ecpD	100.0	99.1	NP_286007	(yagW/ecpD) polymerized tip adhesin of ECP fibers [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00002	214204	216729	+	yagX/ecpC	100.0	98.7	NP_286008	(yagX/ecpC) E. coli common pilus usher EcpC [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00002	213510	214178	+	yagY/ecpB	100.0	98.1	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00002	212865	213452	+	yagZ/ecpA	100.0	99.2	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00020	21361	22320	+	ybtA	100.0	99.9	NP_405473	(ybtA) transcriptional regulator YbtA [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00020	40098	41675	+	ybtE	100.0	99.8	NP_405468	(ybtE) yersiniabactin siderophore biosynthetic protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00020	19392	21194	-	ybtP	100.0	99.7	NP_405474	(ybtP) lipoprotein inner membrane ABC-transporter [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00020	17603	19405	-	ybtQ	100.0	99.8	NP_405475	(ybtQ) inner membrane ABC-transporter YbtQ [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00020	14998	16302	-	ybtS	100.0	97.6	NP_405477	(ybtS) salicylate synthase Irp9 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00020	39291	40094	+	ybtT	100.0	99.9	NP_405469	(ybtT) yersiniabactin biosynthetic protein YbtT [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00020	38194	39294	+	ybtU	100.0	99.6	NP_405470	(ybtU) yersiniabactin biosynthetic protein YbtU [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00020	16330	17610	-	ybtX	100.0	97.7	NP_405476	(ybtX) putative signal transducer [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00002	212200	212790	+	ykgK/ecpR	100.0	97.0	NP_286011	(ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

ID044

Contig	Start	End	Strand	Gene	Coverage	Identity	Accession	Product
contig00022	14725	16153	+	aslA	100.0	93.6	AAG10151	(aslA) putative arylsulfatase [AslA (VF0238)] [Escherichia coli O18:K1:H7 str. RS218]
contig00026	8086	8541	+	csgB	99.8	83.8	NP_460114	(csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00026	6681	7331	-	csgD	100.0	81.1	NP_460113	(csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00026	5846	6262	-	csgF	99.0	81.2	NP_460111	(csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00026	4986	5819	-	csgG	100.0	83.5	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00008	99161	99907	-	entA	100.0	95.7	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00008	99907	100764	-	entB	100.0	98.1	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00008	102398	103585	-	entC	100.0	97.9	NP_752611	(entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00008	118229	118999	+	entD	100.0	95.2	NP_752599	(entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00008	100778	102388	-	entE	100.0	95.5	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00008	110448	114301	-	entF	99.3	95.7	NP_752604	(entF) enterobactin synthase multienzyme complex component ATP-dependent [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00008	104908	106158	-	entS	100.0	95.4	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00066	261	2159	+	espL1	100.0	97.6	NP_288154	(espL1) Type III secretion system effector espL1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00034	37583	39769	+	espL4	100.0	97.3	NP_290644	(espL4) Type III secretion system effector EspL4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00042	23235	24288	+	espR1	83.7	93.8	NP_287686	(espR1) Type III secretion system effector espR1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00003	50497	51918	-	espX1	100.0	93.2	NP_285716	(espX1) Type III secretion system effector EspX1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00034	7787	9367	-	espX4	99.9	93.2	NP_290672	(espX4) Type III secretion system effector EspX4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00021	31391	32683	+	espX5	100.0	97.1	NP_290699	(espX5) Type III secretion system effector EspX5 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00003	90068	90849	+	espY1	99.9	90.4	NP_285753	(espY1) Type III secretion system effector EspY1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00028	41455	45703	-	fdeC	99.9	94.2	YP_002390132	(fdeC) adhesin FdeC [FdeC (VF0506)] [Escherichia coli O45:K1:H7 str. S88]
contig00008	115964	118204	+	fepA	100.0	96.7	NP_752600	(fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00008	103948	104904	+	fepB	100.0	97.5	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00008	108259	109074	+	fepC	100.0	97.3	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00008	106257	107273	+	fepD	100.0	96.1	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00008	107270	108262	+	fepG	100.0	94.0	NP_752607	(fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00008	114519	115721	-	fes	100.0	96.7	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00072	8955	9566	-	fimA	100.0	88.6	NP_757241	(fimA) Type-1 fimbrial protein A chain precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00072	11064	11666	-	fimB	100.0	98.2	NP_757239	(fimB) Type 1 fimbriae Regulatory protein fimB [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00072	7589	8314	-	fimC	100.0	98.9	NP_757243	(fimC) Chaperone protein fimC precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00072	4886	7522	-	fimD	100.0	98.6	NP_757244	(fimD) Outer membrane usher protein fimD precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00072	9993	10587	-	fimE	99.7	99.3	NP_757240	(fimE) Type 1 fimbriae Regulatory protein fimE [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00072	4346	4879	-	fimF	100.0	97.9	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00072	3830	4333	-	fimG	100.0	97.8	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00072	2908	3819	-	fimH	100.0	97.4	NP_757248	(fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00072	8351	8890	-	fimI	100.0	98.7	NP_757242	(fimI) Fimbrin-like protein fimI precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00049	26629	28650	+	fyuA	100.0	100.0	NP_405467	(fyuA) pesticin/yersiniabactin receptor protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00039	16563	17393	+	gspC	100.0	94.7	YP_404599	(gspC) general secretion pathway protein C [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00039	17633	19483	+	gspD	100.0	96.1	YP_404600	(gspD) general secretion pathway protein D [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00039	19483	20976	+	gspE	100.0	96.9	YP_404601	(gspE) general secretion pathway protein E [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00039	20976	22175	+	gspF	100.0	96.0	YP_404602	(gspF) general secretion pathway protein F [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00039	22216	22671	+	gspG	100.0	95.0	YP_404603	(gspG) general secretion pathway protein G [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00039	22708	23237	+	gspH	99.8	94.9	YP_404604	(gspH) general secretion pathway protein H [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00039	23234	23605	+	gspI	100.0	95.2	YP_404605	(gspI) general secretion pathway protein I [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00039	23638	24207	+	gspJ	100.0	96.7	YP_404606	(gspJ) general secretion pathway protein J [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00039	24204	25181	+	gspK	100.0	97.0	YP_404607	(gspK) general secretion pathway protein K [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00039	25496	26356	+	gspL	100.0	97.0	YP_404608	(gspL) general secretion pathway protein L [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00039	26472	26894	+	gspM	100.0	98.3	YP_404609	(gspM) general secretion pathway protein M [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00049	13529	23020	+	irp1	100.0	99.8	NP_405471	(irp1) yersiniabactin biosynthetic protein Irp1 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00049	7334	13441	+	irp2	100.0	99.8	NP_405472	(irp2) yersiniabactin biosynthetic protein Irp2 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00114	1	1462	+	iucA	81.8	94.1	NP_755502	(iucA) aerobactin siderophore biosynthesis protein IucD [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00114	1463	2410	+	iucB	100.0	95.6	NP_755501	(iucB) aerobactin siderophore biosynthesis protein IucB [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00114	2410	4152	+	iucC	100.0	96.0	NP_755500	(iucC) aerobactin siderophore biosynthesis protein IucC [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00001	145352	146392	-	ompA	100.0	98.1	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00070	5439	6192	+	yagV/ecpE	99.7	97.1	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00070	3872	5515	+	yagW/ecpD	100.0	99.1	NP_286007	(yagW/ecpD) polymerized tip adhesin of ECP fibers [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00070	1357	3882	+	yagX/ecpC	100.0	98.8	NP_286008	(yagX/ecpC) E. coli common pilus usher EcpC [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00070	663	1331	+	yagY/ecpB	100.0	98.1	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00070	18	605	+	yagZ/ecpA	100.0	99.0	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00049	6184	7143	+	ybtA	100.0	99.8	NP_405473	(ybtA) transcriptional regulator YbtA [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00049	24921	26498	+	ybtE	100.0	99.8	NP_405468	(ybtE) yersiniabactin siderophore biosynthetic protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00049	4215	6017	-	ybtP	100.0	99.7	NP_405474	(ybtP) lipoprotein inner membrane ABC-transporter [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00049	2426	4228	-	ybtQ	100.0	99.8	NP_405475	(ybtQ) inner membrane ABC-transporter YbtQ [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00049	1	1125	-	ybtS	86.2	97.9	NP_405477	(ybtS) salicylate synthase Irp9 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00049	24114	24917	+	ybtT	100.0	99.6	NP_405469	(ybtT) yersiniabactin biosynthetic protein YbtT [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00049	23017	24117	+	ybtU	100.0	99.7	NP_405470	(ybtU) yersiniabactin biosynthetic protein YbtU [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00049	1153	2433	-	ybtX	100.0	97.7	NP_405476	(ybtX) putative signal transducer [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00028	48725	49315	+	ykgK/ecpR	100.0	97.0	NP_286011	(ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

ID046II

Contig	Start	End	Strand	Gene	Coverage	Identity	Accession	Product
contig00114	2881	4309	+	aslA	100.0	97.3	AAG10151	(aslA) putative arylsulfatase [AslA (VF0238)] [Escherichia coli O18:K1:H7 str. RS218]
contig00775	147	602	-	csgB	99.8	83.6	NP_460114	(csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00775	1357	2007	+	csgD	100.0	81.3	NP_460113	(csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00590	296	712	+	csgF	99.0	81.2	NP_460111	(csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00590	739	1572	+	csgG	100.0	83.5	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00284	2608	3465	+	entB	100.0	98.4	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00291	2608	3465	+	entB	100.0	98.1	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00284	1	974	+	entC	82.0	97.0	NP_752611	(entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00291	1	974	+	entC	82.0	97.5	NP_752611	(entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00301	106	876	-	entD	100.0	94.3	NP_752599	(entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00284	984	2594	+	entE	100.0	95.8	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00291	984	2594	+	entE	100.0	95.4	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00539	1515	2684	-	entS	93.5	95.8	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00875	766	1935	-	entS	93.5	95.1	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00301	901	3141	-	fepA	100.0	96.8	NP_752600	(fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00539	555	1511	+	fepB	100.0	97.0	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00203	1616	2431	-	fepC	100.0	97.3	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00203	3417	4433	-	fepD	100.0	96.7	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig01996	1	872	+	fepD	85.7	95.6	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00203	2428	3420	-	fepG	100.0	94.1	NP_752607	(fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00210	3884	4489	-	fimA	100.0	90.3	NP_757241	(fimA) Type-1 fimbrial protein A chain precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00026	1253	1855	-	fimB	100.0	97.8	NP_757239	(fimB) Type 1 fimbriae Regulatory protein fimB [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00210	2518	3243	-	fimC	100.0	98.3	NP_757243	(fimC) Chaperone protein fimC precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00210	1	2451	-	fimD	93.0	97.9	NP_757244	(fimD) Outer membrane usher protein fimD precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00026	179	775	-	fimE	100.0	99.0	NP_757240	(fimE) Type 1 fimbriae Regulatory protein fimE [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig01077	1	429	+	fimF	80.3	97.4	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig01079	1	429	+	fimF	80.3	97.2	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig01077	442	945	+	fimG	100.0	97.4	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig01079	442	945	+	fimG	100.0	98.4	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00210	3280	3819	-	fimI	100.0	99.1	NP_757242	(fimI) Fimbrin-like protein fimI precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00003	31335	32165	+	gspC	100.0	95.2	YP_404599	(gspC) general secretion pathway protein C [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00003	32405	34255	+	gspD	100.0	97.1	YP_404600	(gspD) general secretion pathway protein D [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00003	34255	35748	+	gspE	100.0	96.5	YP_404601	(gspE) general secretion pathway protein E [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00003	35748	36947	+	gspF	100.0	96.1	YP_404602	(gspF) general secretion pathway protein F [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00003	36988	37443	+	gspG	100.0	95.0	YP_404603	(gspG) general secretion pathway protein G [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00003	37480	38010	+	gspH	100.0	95.5	YP_404604	(gspH) general secretion pathway protein H [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00003	38007	38378	+	gspI	100.0	95.2	YP_404605	(gspI) general secretion pathway protein I [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig01244	1153	1452	-	gspI	80.7	94.3	YP_404605	(gspI) general secretion pathway protein I [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00003	38411	38980	+	gspJ	100.0	96.5	YP_404606	(gspJ) general secretion pathway protein J [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig01244	551	1120	-	gspJ	100.0	97.2	YP_404606	(gspJ) general secretion pathway protein J [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig01483	742	1164	+	gspM	100.0	94.8	YP_404609	(gspM) general secretion pathway protein M [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig02105	464	805	-	gspM	80.8	97.4	YP_404609	(gspM) general secretion pathway protein M [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00096	175	537	+	gtrA	100.0	90.4	NP_706257	(gtrA) bactoprenol-linked glucose translocase/flippase [LPS (VF0124)] [Shigella flexneri 2a str. 301]
contig01309	471	1385	-	ompA	86.7	94.0	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00011	17098	17851	+	yagV/ecpE	99.7	97.3	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00011	15531	17174	+	yagW/ecpD	100.0	99.0	NP_286007	(yagW/ecpD) polymerized tip adhesin of ECP fibers [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00011	13016	15541	+	yagX/ecpC	100.0	98.8	NP_286008	(yagX/ecpC) E. coli common pilus usher EcpC [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00011	12322	12990	+	yagY/ecpB	100.0	97.6	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00011	11677	12264	+	yagZ/ecpA	100.0	99.3	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00011	11012	11602	+	ykgK/ecpR	100.0	97.3	NP_286011	(ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

ID049

Contig	Start	End	Strand	Gene	Coverage	Identity	Accession	Product
contig00090	5232	5976	-	afaB-I	100.0	98.2	CAW30798	(afaB-I) chaperone AfaB [Afimbrial adhesin AFA-I mannose-resistant adhesin (AI010)] [Escherichia coli O25b:H4 str. FV9863]
contig00090	2557	5139	-	afaC-I	100.0	99.0	CAW30799	(afaC-I) usher AfaC [Afimbrial adhesin AFA-I mannose-resistant adhesin (AI010)] [Escherichia coli O25b:H4 str. FV9863]
contig00014	49394	50822	+	aslA	100.0	92.9	AAG10151	(aslA) putative arylsulfatase [AslA (VF0238)] [Escherichia coli O18:K1:H7 str. RS218]
contig00010	22899	23354	+	csgB	99.8	83.6	NP_460114	(csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00010	21494	22144	-	csgD	100.0	81.3	NP_460113	(csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00010	20659	21075	-	csgF	99.0	81.2	NP_460111	(csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00010	19799	20632	-	csgG	100.0	83.5	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00090	7338	7565	+	daaF	100.0	100.0	AAA23662	(daaF) DaaF protein [F1845 fimbrial adhesin (AI016)] [Escherichia coli str. C1845]
contig00090	6230	6535	-	draA	100.0	100.0	AAK16475	(draA) cytoplamic protein DraA [Dr adhesins (VF0223)] [Escherichia coli O75:K5:H- str. IH11128]
contig00090	2098	2541	-	draD	100.0	99.8	AAK16478	(draD) DraD periplasmic protein [Dr adhesins (VF0223)] [Escherichia coli O75:K5:H- str. IH11128]
contig00090	800	1359	-	draE2	99.6	99.6	AAB65153	(draE2) Dr-II structural adhesin precursor [Afa/Dr family (VF0212)] [Escherichia coli EC7372]
contig00090	1546	1719	-	draP	100.0	99.4	AAK16479	(draP) DraP [Dr adhesins (VF0223)] [Escherichia coli O75:K5:H- str. IH11128]
contig00024	47219	47965	-	entA	100.0	95.5	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00024	47965	48822	-	entB	100.0	98.1	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00024	50456	51643	-	entC	100.0	97.8	NP_752611	(entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00024	66287	67057	+	entD	100.0	95.2	NP_752599	(entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00024	48836	50446	-	entE	100.0	95.4	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00024	58506	62359	-	entF	99.3	95.6	NP_752604	(entF) enterobactin synthase multienzyme complex component ATP-dependent [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00024	52966	54216	-	entS	100.0	95.4	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00030	18433	20332	+	espL1	100.0	97.6	NP_288154	(espL1) Type III secretion system effector espL1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00026	50708	51762	+	espR1	83.7	94.1	NP_287686	(espR1) Type III secretion system effector espR1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00003	131705	133127	+	espX1	100.0	95.2	NP_285716	(espX1) Type III secretion system effector EspX1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00004	27956	29536	+	espX4	100.0	96.2	NP_290672	(espX4) Type III secretion system effector EspX4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00004	59040	60332	-	espX5	100.0	97.1	NP_290699	(espX5) Type III secretion system effector EspX5 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00070	15813	20061	-	fdeC	99.9	94.2	YP_002390132	(fdeC) adhesin FdeC [FdeC (VF0506)] [Escherichia coli O45:K1:H7 str. S88]
contig00024	64022	66262	+	fepA	100.0	96.7	NP_752600	(fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00024	52006	52962	+	fepB	100.0	97.5	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00024	56317	57132	+	fepC	100.0	97.2	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00024	54315	55331	+	fepD	100.0	96.1	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00024	55328	56320	+	fepG	100.0	94.1	NP_752607	(fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00024	62577	63779	-	fes	100.0	96.7	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00034	24982	25586	-	fimA	99.8	90.8	NP_757241	(fimA) Type-1 fimbrial protein A chain precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00034	27084	27686	-	fimB	100.0	97.8	NP_757239	(fimB) Type 1 fimbriae Regulatory protein fimB [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00034	23616	24341	-	fimC	100.0	98.9	NP_757243	(fimC) Chaperone protein fimC precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00034	20913	23549	-	fimD	100.0	98.3	NP_757244	(fimD) Outer membrane usher protein fimD precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00034	26010	26606	-	fimE	100.0	98.8	NP_757240	(fimE) Type 1 fimbriae Regulatory protein fimE [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00034	20373	20906	-	fimF	100.0	97.9	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00034	19857	20360	-	fimG	100.0	97.4	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00034	18935	19846	-	fimH	100.0	97.6	NP_757248	(fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00034	24378	24917	-	fimI	100.0	98.5	NP_757242	(fimI) Fimbrin-like protein fimI precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00102	7917	9938	+	fyuA	100.0	100.0	NP_405467	(fyuA) pesticin/yersiniabactin receptor protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00028	9962	10792	-	gspC	100.0	95.4	YP_404599	(gspC) general secretion pathway protein C [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00028	7872	9722	-	gspD	100.0	95.5	YP_404600	(gspD) general secretion pathway protein D [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00028	6379	7872	-	gspE	100.0	96.4	YP_404601	(gspE) general secretion pathway protein E [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00028	5180	6379	-	gspF	100.0	95.4	YP_404602	(gspF) general secretion pathway protein F [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00028	4684	5139	-	gspG	100.0	96.3	YP_404603	(gspG) general secretion pathway protein G [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00028	4117	4647	-	gspH	100.0	95.3	YP_404604	(gspH) general secretion pathway protein H [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00028	3749	4120	-	gspI	100.0	94.6	YP_404605	(gspI) general secretion pathway protein I [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00028	3147	3716	-	gspJ	100.0	94.7	YP_404606	(gspJ) general secretion pathway protein J [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00028	2173	3150	-	gspK	100.0	97.1	YP_404607	(gspK) general secretion pathway protein K [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00028	998	1858	-	gspL	100.0	94.8	YP_404608	(gspL) general secretion pathway protein L [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00028	460	882	-	gspM	100.0	92.9	YP_404609	(gspM) general secretion pathway protein M [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00056	17866	23973	+	irp2	100.0	99.7	NP_405472	(irp2) yersiniabactin biosynthetic protein Irp2 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00085	7311	9098	+	iucA	100.0	94.3	NP_755502	(iucA) aerobactin siderophore biosynthesis protein IucD [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00085	9099	10046	+	iucB	100.0	95.7	NP_755501	(iucB) aerobactin siderophore biosynthesis protein IucB [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00085	10046	11788	+	iucC	100.0	96.1	NP_755500	(iucC) aerobactin siderophore biosynthesis protein IucC [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00085	11785	13106	+	iucD	98.8	96.3	NP_755499	(iucD) L-lysine 6-monooxygenase IucD [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00085	13044	15345	+	iutA	100.0	88.4	NP_755498	(iutA) ferric aerobactin receptor precusor IutA [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00039	15985	17025	-	ompA	100.0	98.1	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00142	957	1508	+	papX	100.0	97.5	NP_755457	(papX) PapX protein regulates flagellum synthesis to repress motility [P fimbriae (CVF425)] [Escherichia coli CFT073]
contig00056	16716	17675	+	ybtA	100.0	99.7	NP_405473	(ybtA) transcriptional regulator YbtA [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00102	6209	7786	+	ybtE	100.0	99.7	NP_405468	(ybtE) yersiniabactin siderophore biosynthetic protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00056	14747	16549	-	ybtP	100.0	99.6	NP_405474	(ybtP) lipoprotein inner membrane ABC-transporter [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00056	12958	14760	-	ybtQ	100.0	99.9	NP_405475	(ybtQ) inner membrane ABC-transporter YbtQ [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00056	10353	11657	-	ybtS	100.0	97.7	NP_405477	(ybtS) salicylate synthase Irp9 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00102	5402	6205	+	ybtT	100.0	99.6	NP_405469	(ybtT) yersiniabactin biosynthetic protein YbtT [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00102	4305	5405	+	ybtU	100.0	99.6	NP_405470	(ybtU) yersiniabactin biosynthetic protein YbtU [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00056	11685	12965	-	ybtX	100.0	97.6	NP_405476	(ybtX) putative signal transducer [Yersiniabactin (VF0136)] [Yersinia pestis CO92]

ID051

Contig	Start	End	Strand	Gene	Coverage	Identity	Accession	Product
contig00023	73361	73666	-	afaA	100.0	100.0	CAW30797	(afaA) fimbrial major subunit AfaA [Afimbrial adhesin AFA-I mannose-resistant adhesin (AI010)] [Escherichia coli O25b:H4 str. FV9863]
contig00023	72326	73070	-	afaB-I	100.0	99.6	CAW30798	(afaB-I) chaperone AfaB [Afimbrial adhesin AFA-I mannose-resistant adhesin (AI010)] [Escherichia coli O25b:H4 str. FV9863]
contig00023	69651	72233	-	afaC-I	100.0	99.9	CAW30799	(afaC-I) usher AfaC [Afimbrial adhesin AFA-I mannose-resistant adhesin (AI010)] [Escherichia coli O25b:H4 str. FV9863]
contig00023	69192	69635	-	afaD	100.0	100.0	CAW30800	(afaD) AfaD [Afimbrial adhesin AFA-I mannose-resistant adhesin (AI010)] [Escherichia coli O25b:H4 str. FV9863]
contig00023	67954	68439	-	afaE-I	100.0	99.8	CAW30801	(afaE-I) AFA-I adhesin [Afa/Dr family (VF0212)] [Escherichia coli O25b:H4 str. FV9863]
contig00019	71053	72481	+	aslA	100.0	98.2	AAG10151	(aslA) putative arylsulfatase [AslA (VF0238)] [Escherichia coli O18:K1:H7 str. RS218]
contig00028	16900	18846	+	chuA	100.0	99.5	NP_756170	(chuA) Outer membrane heme/hemoglobin receptor ChuA [Chu (VF0227)] [Escherichia coli CFT073]
contig00028	18895	19923	+	chuS	100.0	99.0	NP_756169	(chuS) heme oxygenase ChuS [Chu (VF0227)] [Escherichia coli CFT073]
contig00028	15266	16258	-	chuT	100.0	99.8	NP_756175	(chuT) periplasmic heme-binding protein ChuT [Chu (VF0227)] [Escherichia coli CFT073]
contig00028	11738	12730	-	chuU	100.0	99.5	NP_756179	(chuU) heme permease protein ChuU [Chu (VF0227)] [Escherichia coli CFT073]
contig00028	10971	11771	-	chuV	100.0	99.8	NP_756180	(chuV) ATP-binding hydrophilic protein ChuV [Chu (VF0227)] [Escherichia coli CFT073]
contig00028	13909	15246	-	chuW	100.0	98.9	NP_756176	(chuW) Putative oxygen independent coproporphyrinogen III oxidase [Chu (VF0227)] [Escherichia coli CFT073]
contig00028	13402	13896	-	chuX	100.0	100.0	NP_756177	(chuX) putative heme-binding protein ChuX [Chu (VF0227)] [Escherichia coli CFT073]
contig00028	12779	13402	-	chuY	100.0	98.2	NP_756178	(chuY) ChuY [Chu (VF0227)] [Escherichia coli CFT073]
contig00009	133806	134261	-	csgB	99.8	83.8	NP_460114	(csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00009	135014	135664	+	csgD	100.0	81.6	NP_460113	(csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00009	136083	136499	+	csgF	99.0	80.8	NP_460111	(csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00009	136526	137359	+	csgG	100.0	83.2	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00023	74584	74811	+	daaF	100.0	100.0	AAA23662	(daaF) DaaF protein [F1845 fimbrial adhesin (AI016)] [Escherichia coli str. C1845]
contig00023	68641	68814	-	draP	100.0	98.8	AAK16479	(draP) DraP [Dr adhesins (VF0223)] [Escherichia coli O75:K5:H- str. IH11128]
contig00002	281539	282285	-	entA	100.0	98.1	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00002	282285	283142	-	entB	100.0	99.4	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00002	284776	285963	-	entC	100.0	98.7	NP_752611	(entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00002	300452	301113	+	entD	85.9	96.7	NP_752599	(entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00002	283156	284766	-	entE	100.0	98.9	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00002	292643	296524	-	entF	100.0	98.2	NP_752604	(entF) enterobactin synthase multienzyme complex component ATP-dependent [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00002	287100	288350	-	entS	100.0	97.4	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00006	228839	233086	-	fdeC	99.9	97.4	YP_002390132	(fdeC) adhesin FdeC [FdeC (VF0506)] [Escherichia coli O45:K1:H7 str. S88]
contig00002	298187	300427	+	fepA	100.0	98.9	NP_752600	(fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00002	286140	287096	+	fepB	100.0	98.4	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00002	290451	291266	+	fepC	100.0	99.1	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00002	288449	289465	+	fepD	100.0	97.8	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00002	289462	290454	+	fepG	100.0	97.9	NP_752607	(fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00002	296742	297944	-	fes	100.0	99.0	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00003	331496	332100	-	fimA	99.8	90.8	NP_757241	(fimA) Type-1 fimbrial protein A chain precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00003	330130	330855	-	fimC	100.0	98.9	NP_757243	(fimC) Chaperone protein fimC precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00003	327427	330063	-	fimD	100.0	98.5	NP_757244	(fimD) Outer membrane usher protein fimD precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00003	332523	333119	-	fimE	100.0	98.8	NP_757240	(fimE) Type 1 fimbriae Regulatory protein fimE [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00003	326887	327420	-	fimF	100.0	96.6	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00003	326371	326874	-	fimG	100.0	98.2	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00003	325449	326360	-	fimH	100.0	97.5	NP_757248	(fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00003	330892	331431	-	fimI	100.0	98.5	NP_757242	(fimI) Fimbrin-like protein fimI precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00033	7952	9973	+	fyuA	100.0	99.8	NP_405467	(fyuA) pesticin/yersiniabactin receptor protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00008	167409	168239	+	gspC	100.0	93.9	YP_404599	(gspC) general secretion pathway protein C [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00008	168479	170329	+	gspD	100.0	96.1	YP_404600	(gspD) general secretion pathway protein D [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00008	170329	171822	+	gspE	100.0	95.0	YP_404601	(gspE) general secretion pathway protein E [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00008	171822	173021	+	gspF	100.0	94.2	YP_404602	(gspF) general secretion pathway protein F [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00008	173062	173517	+	gspG	100.0	96.0	YP_404603	(gspG) general secretion pathway protein G [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00008	173554	174084	+	gspH	100.0	94.7	YP_404604	(gspH) general secretion pathway protein H [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00008	174081	174452	+	gspI	100.0	92.2	YP_404605	(gspI) general secretion pathway protein I [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00008	174485	175054	+	gspJ	100.0	94.4	YP_404606	(gspJ) general secretion pathway protein J [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00008	175051	176028	+	gspK	100.0	96.6	YP_404607	(gspK) general secretion pathway protein K [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00008	176343	177203	+	gspL	100.0	94.8	YP_404608	(gspL) general secretion pathway protein L [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00008	177319	177740	+	gspM	99.8	92.9	YP_404609	(gspM) general secretion pathway protein M [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00036	11815	17922	+	irp2	100.0	99.4	NP_405472	(irp2) yersiniabactin biosynthetic protein Irp2 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00035	8835	10616	+	iucA	100.0	99.8	NP_709454	(iucA) aerobactin synthesis protein IucA [Aerobactin (VF0123)] [Shigella flexneri 2a str. 301]
contig00035	10617	11564	+	iucB	100.0	99.8	NP_709455	(iucB) aerobactin synthesis protein IucB [Aerobactin (VF0123)] [Shigella flexneri 2a str. 301]
contig00035	11564	13306	+	iucC	100.0	98.2	NP_755500	(iucC) aerobactin siderophore biosynthesis protein IucC [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00035	13303	14624	+	iucD	98.8	96.3	NP_755499	(iucD) L-lysine 6-monooxygenase IucD [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00035	14562	16863	+	iutA	100.0	88.4	NP_755498	(iutA) ferric aerobactin receptor precusor IutA [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00008	192461	194137	-	kpsD	100.0	98.3	AAA21682	(kpsD) KpsD [K1 capsule (VF0239)] [Escherichia coli O18:K1:H7 str. RS218]
contig00008	178799	179575	+	kpsM	100.0	94.7	AAA24046	(kpsM) KpsM [K1 capsule (VF0239)] [Escherichia coli O18:K1:H7 str. RS218]
contig00017	1055	2107	+	ompA	100.0	95.8	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00035	749	1062	-	papB	99.7	98.4		(papB) regulatory protein PapB [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig00035	1467	1700	+	papI	100.0	94.9	NP_755468	(papI) regulatory protein PapI [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig00074	256	807	+	papX	100.0	97.6	NP_755457	(papX) PapX protein regulates flagellum synthesis to repress motility [P fimbriae (CVF425)] [Escherichia coli CFT073]
contig00035	17795	21694	+	sat	100.0	99.6	NP_755494	(sat) Aecreted auto transpoter toxin [Sat (VF0231)] [Escherichia coli CFT073]
contig00047	8392	9530	+	senB	99.9	99.7	YP_406304	(senB) enterotoxin [ShET2 (VF0258)] [Shigella flexneri 2a str. 301]
contig00006	248424	249177	+	yagV/ecpE	99.7	98.0	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00006	246857	248500	+	yagW/ecpD	100.0	99.2	NP_286007	(yagW/ecpD) polymerized tip adhesin of ECP fibers [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00006	244342	246867	+	yagX/ecpC	100.0	97.6	NP_286008	(yagX/ecpC) E. coli common pilus usher EcpC [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00006	243648	244316	+	yagY/ecpB	100.0	98.1	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00006	243004	243591	+	yagZ/ecpA	100.0	98.5	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00036	10665	11624	+	ybtA	100.0	99.3	NP_405473	(ybtA) transcriptional regulator YbtA [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00033	6244	7821	+	ybtE	100.0	99.8	NP_405468	(ybtE) yersiniabactin siderophore biosynthetic protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00036	8696	10498	-	ybtP	100.0	99.6	NP_405474	(ybtP) lipoprotein inner membrane ABC-transporter [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00036	6907	8709	-	ybtQ	100.0	99.6	NP_405475	(ybtQ) inner membrane ABC-transporter YbtQ [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00036	4302	5606	-	ybtS	100.0	99.8	NP_405477	(ybtS) salicylate synthase Irp9 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00033	5437	6240	+	ybtT	100.0	99.6	NP_405469	(ybtT) yersiniabactin biosynthetic protein YbtT [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00033	4340	5440	+	ybtU	100.0	99.7	NP_405470	(ybtU) yersiniabactin biosynthetic protein YbtU [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00036	5634	6914	-	ybtX	100.0	99.7	NP_405476	(ybtX) putative signal transducer [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00006	242339	242929	+	ykgK/ecpR	100.0	99.5	NP_286011	(ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

ID054

Contig	Start	End	Strand	Gene	Coverage	Identity	Accession	Product
contig00014	107924	108379	-	csgB	99.8	84.0	NP_460114	(csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00014	109133	109783	+	csgD	100.0	81.1	NP_460113	(csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00014	110202	110618	+	csgF	99.0	81.2	NP_460111	(csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00014	110645	111478	+	csgG	100.0	83.1	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00013	99574	100320	-	entA	100.0	96.0	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00013	100320	101177	-	entB	100.0	97.9	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00013	102811	103998	-	entC	100.0	97.5	NP_752611	(entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00013	118642	119412	+	entD	100.0	94.0	NP_752599	(entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00013	101191	102801	-	entE	100.0	95.8	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00013	110885	114714	-	entF	98.7	95.4	NP_752604	(entF) enterobactin synthase multienzyme complex component ATP-dependent [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00013	105321	106571	-	entS	100.0	95.6	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00005	74456	76324	-	espL1	98.4	95.3	NP_288154	(espL1) Type III secretion system effector espL1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00031	24866	25921	+	espR1	83.8	94.2	NP_287686	(espR1) Type III secretion system effector espR1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00006	200479	201899	+	espX1	99.9	94.7	NP_285716	(espX1) Type III secretion system effector EspX1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00017	55541	57121	-	espX4	99.9	93.1	NP_290672	(espX4) Type III secretion system effector EspX4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00017	24730	26022	+	espX5	100.0	95.7	NP_290699	(espX5) Type III secretion system effector EspX5 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00022	43044	47285	-	fdeC	99.8	92.4	YP_002390132	(fdeC) adhesin FdeC [FdeC (VF0506)] [Escherichia coli O45:K1:H7 str. S88]
contig00013	116377	118617	+	fepA	100.0	96.8	NP_752600	(fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00013	104361	105317	+	fepB	100.0	97.4	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00013	108672	109487	+	fepC	100.0	97.3	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00013	106670	107686	+	fepD	100.0	96.0	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00013	107683	108675	+	fepG	100.0	94.0	NP_752607	(fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00013	114932	116134	-	fes	100.0	96.8	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00015	107592	108196	-	fimA	99.8	90.6	NP_757241	(fimA) Type-1 fimbrial protein A chain precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00032	39377	39979	+	fimB	100.0	97.8	NP_757239	(fimB) Type 1 fimbriae Regulatory protein fimB [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00015	106220	106945	-	fimC	100.0	98.6	NP_757243	(fimC) Chaperone protein fimC precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00015	103517	106153	-	fimD	100.0	98.7	NP_757244	(fimD) Outer membrane usher protein fimD precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00032	40457	41053	+	fimE	100.0	99.2	NP_757240	(fimE) Type 1 fimbriae Regulatory protein fimE [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00015	102977	103510	-	fimF	100.0	96.6	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00015	102461	102964	-	fimG	100.0	97.8	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00015	101539	102450	-	fimH	100.0	97.7	NP_757248	(fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00015	106988	107527	-	fimI	100.0	99.1	NP_757242	(fimI) Fimbrin-like protein fimI precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00001	382695	383525	-	gspC	100.0	95.1	YP_404599	(gspC) general secretion pathway protein C [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	380605	382455	-	gspD	100.0	97.0	YP_404600	(gspD) general secretion pathway protein D [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	379112	380605	-	gspE	100.0	97.1	YP_404601	(gspE) general secretion pathway protein E [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	377913	379112	-	gspF	100.0	96.2	YP_404602	(gspF) general secretion pathway protein F [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	377417	377872	-	gspG	100.0	95.6	YP_404603	(gspG) general secretion pathway protein G [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	376850	377380	-	gspH	100.0	96.0	YP_404604	(gspH) general secretion pathway protein H [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	376482	376853	-	gspI	100.0	95.2	YP_404605	(gspI) general secretion pathway protein I [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	375880	376449	-	gspJ	100.0	97.2	YP_404606	(gspJ) general secretion pathway protein J [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	374906	375883	-	gspK	100.0	96.1	YP_404607	(gspK) general secretion pathway protein K [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	373731	374591	-	gspL	100.0	97.6	YP_404608	(gspL) general secretion pathway protein L [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	373193	373615	-	gspM	100.0	94.1	YP_404609	(gspM) general secretion pathway protein M [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00009	104181	105233	-	ompA	100.0	94.3	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00022	56391	57144	+	yagV/ecpE	99.7	96.8	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00022	54824	56467	+	yagW/ecpD	100.0	98.5	NP_286007	(yagW/ecpD) polymerized tip adhesin of ECP fibers [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00022	52309	54834	+	yagX/ecpC	100.0	98.7	NP_286008	(yagX/ecpC) E. coli common pilus usher EcpC [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00022	51615	52283	+	yagY/ecpB	100.0	98.7	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00022	50970	51557	+	yagZ/ecpA	100.0	99.3	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00022	50305	50895	+	ykgK/ecpR	100.0	97.6	NP_286011	(ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

ID057

Contig	Start	End	Strand	Gene	Coverage	Identity	Accession	Product
contig00010	164910	165215	-	afaA	100.0	100.0	CAW30797	(afaA) fimbrial major subunit AfaA [Afimbrial adhesin AFA-I mannose-resistant adhesin (AI010)] [Escherichia coli O25b:H4 str. FV9863]
contig00010	163896	164640	-	afaB-I	100.0	99.6	CAW30798	(afaB-I) chaperone AfaB [Afimbrial adhesin AFA-I mannose-resistant adhesin (AI010)] [Escherichia coli O25b:H4 str. FV9863]
contig00010	161221	163803	-	afaC-I	100.0	99.9	CAW30799	(afaC-I) usher AfaC [Afimbrial adhesin AFA-I mannose-resistant adhesin (AI010)] [Escherichia coli O25b:H4 str. FV9863]
contig00010	160762	161205	-	afaD	100.0	100.0	CAW30800	(afaD) AfaD [Afimbrial adhesin AFA-I mannose-resistant adhesin (AI010)] [Escherichia coli O25b:H4 str. FV9863]
contig00010	159524	160009	-	afaE-I	100.0	99.8	CAW30801	(afaE-I) AFA-I adhesin [Afa/Dr family (VF0212)] [Escherichia coli O25b:H4 str. FV9863]
contig00015	97772	98227	-	csgB	99.8	83.8	NP_460114	(csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00068	615	1031	+	csgF	99.0	81.2	NP_460111	(csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00068	1058	1891	+	csgG	100.0	83.0	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00010	166133	166360	+	daaF	100.0	100.0	AAA23662	(daaF) DaaF protein [F1845 fimbrial adhesin (AI016)] [Escherichia coli str. C1845]
contig00010	160211	160384	-	draP	100.0	98.8	AAK16479	(draP) DraP [Dr adhesins (VF0223)] [Escherichia coli O75:K5:H- str. IH11128]
contig00006	212521	213267	+	entA	100.0	96.0	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00006	211664	212521	+	entB	100.0	97.9	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00006	208843	210030	+	entC	100.0	97.5	NP_752611	(entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00006	193429	194199	-	entD	100.0	95.1	NP_752599	(entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00006	210040	211650	+	entE	100.0	95.8	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00006	198127	201956	+	entF	98.7	95.5	NP_752604	(entF) enterobactin synthase multienzyme complex component ATP-dependent [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00006	206270	207520	+	entS	100.0	95.5	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00011	70920	72789	-	espL1	98.5	95.2	NP_288154	(espL1) Type III secretion system effector espL1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00035	25977	27031	+	espR1	83.7	94.2	NP_287686	(espR1) Type III secretion system effector espR1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00005	127832	129252	+	espX1	99.9	94.6	NP_285716	(espX1) Type III secretion system effector EspX1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00020	26196	27776	-	espX4	99.9	92.9	NP_290672	(espX4) Type III secretion system effector EspX4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00036	5440	6732	-	espX5	100.0	95.6	NP_290699	(espX5) Type III secretion system effector EspX5 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00013	71577	75825	-	fdeC	99.9	94.2	YP_002390132	(fdeC) adhesin FdeC [FdeC (VF0506)] [Escherichia coli O45:K1:H7 str. S88]
contig00006	194224	196464	-	fepA	100.0	97.5	NP_752600	(fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00006	207524	208480	-	fepB	100.0	97.4	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00006	203354	204169	-	fepC	100.0	97.3	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00006	205155	206171	-	fepD	100.0	96.4	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00006	204166	205158	-	fepG	100.0	94.5	NP_752607	(fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00006	196707	197909	+	fes	100.0	96.3	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00005	244087	244692	-	fimA	100.0	90.1	NP_757241	(fimA) Type-1 fimbrial protein A chain precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00005	246190	246792	-	fimB	100.0	97.8	NP_757239	(fimB) Type 1 fimbriae Regulatory protein fimB [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00005	242721	243446	-	fimC	100.0	98.3	NP_757243	(fimC) Chaperone protein fimC precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00005	240018	242654	-	fimD	100.0	98.6	NP_757244	(fimD) Outer membrane usher protein fimD precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00005	245116	245712	-	fimE	100.0	99.0	NP_757240	(fimE) Type 1 fimbriae Regulatory protein fimE [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00005	239478	240011	-	fimF	100.0	97.4	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00005	238962	239465	-	fimG	100.0	98.4	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00005	238040	238951	-	fimH	100.0	97.3	NP_757248	(fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00005	243483	244022	-	fimI	100.0	98.9	NP_757242	(fimI) Fimbrin-like protein fimI precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00023	40394	42415	+	fyuA	100.0	99.9	NP_405467	(fyuA) pesticin/yersiniabactin receptor protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00001	133759	134736	-	gspK	100.0	97.7	YP_404607	(gspK) general secretion pathway protein K [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	132584	133444	-	gspL	100.0	96.9	YP_404608	(gspL) general secretion pathway protein L [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	132046	132468	-	gspM	100.0	97.2	YP_404609	(gspM) general secretion pathway protein M [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00023	27293	36784	+	irp1	100.0	99.7	NP_405471	(irp1) yersiniabactin biosynthetic protein Irp1 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00023	21098	27205	+	irp2	100.0	99.7	NP_405472	(irp2) yersiniabactin biosynthetic protein Irp2 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00051	7017	8804	+	iucA	100.0	94.2	NP_755502	(iucA) aerobactin siderophore biosynthesis protein IucD [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00051	8805	9752	+	iucB	100.0	95.6	NP_755501	(iucB) aerobactin siderophore biosynthesis protein IucB [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00051	9752	11494	+	iucC	100.0	96.0	NP_755500	(iucC) aerobactin siderophore biosynthesis protein IucC [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00051	11491	12812	+	iucD	98.8	96.3	NP_755499	(iucD) L-lysine 6-monooxygenase IucD [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00051	12750	15051	+	iutA	100.0	88.4	NP_755498	(iutA) ferric aerobactin receptor precusor IutA [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00003	186194	187246	-	ompA	100.0	94.5	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00062	7729	8867	+	senB	99.9	99.7	YP_406304	(senB) enterotoxin [ShET2 (VF0258)] [Shigella flexneri 2a str. 301]
contig00013	84931	85684	+	yagV/ecpE	99.7	96.8	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00013	83364	85007	+	yagW/ecpD	100.0	98.7	NP_286007	(yagW/ecpD) polymerized tip adhesin of ECP fibers [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00013	80849	83374	+	yagX/ecpC	100.0	98.7	NP_286008	(yagX/ecpC) E. coli common pilus usher EcpC [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00013	80155	80823	+	yagY/ecpB	100.0	98.8	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00013	79510	80097	+	yagZ/ecpA	100.0	99.3	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00023	19948	20907	+	ybtA	100.0	99.5	NP_405473	(ybtA) transcriptional regulator YbtA [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00023	38685	40262	+	ybtE	100.0	99.6	NP_405468	(ybtE) yersiniabactin siderophore biosynthetic protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00023	17979	19781	-	ybtP	100.0	99.6	NP_405474	(ybtP) lipoprotein inner membrane ABC-transporter [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00023	16190	17992	-	ybtQ	100.0	99.7	NP_405475	(ybtQ) inner membrane ABC-transporter YbtQ [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00023	13585	14889	-	ybtS	100.0	99.7	NP_405477	(ybtS) salicylate synthase Irp9 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00023	37878	38681	+	ybtT	100.0	99.4	NP_405469	(ybtT) yersiniabactin biosynthetic protein YbtT [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00023	36781	37881	+	ybtU	100.0	99.5	NP_405470	(ybtU) yersiniabactin biosynthetic protein YbtU [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00023	14917	16197	-	ybtX	100.0	99.6	NP_405476	(ybtX) putative signal transducer [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00013	78845	79435	+	ykgK/ecpR	100.0	97.3	NP_286011	(ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

ID066II

Contig	Start	End	Strand	Gene	Coverage	Identity	Accession	Product
contig00207	4654	6082	+	aslA	100.0	93.5	AAG10151	(aslA) putative arylsulfatase [AslA (VF0238)] [Escherichia coli O18:K1:H7 str. RS218]
contig00739	348	1776	+	aslA	100.0	98.5	AAG10151	(aslA) putative arylsulfatase [AslA (VF0238)] [Escherichia coli O18:K1:H7 str. RS218]
contig00099	8505	10451	+	chuA	100.0	99.7	NP_756170	(chuA) Outer membrane heme/hemoglobin receptor ChuA [Chu (VF0227)] [Escherichia coli CFT073]
contig00099	10500	11528	+	chuS	100.0	99.5	NP_756169	(chuS) heme oxygenase ChuS [Chu (VF0227)] [Escherichia coli CFT073]
contig00099	6871	7863	-	chuT	100.0	99.7	NP_756175	(chuT) periplasmic heme-binding protein ChuT [Chu (VF0227)] [Escherichia coli CFT073]
contig00099	3343	4335	-	chuU	100.0	99.5	NP_756179	(chuU) heme permease protein ChuU [Chu (VF0227)] [Escherichia coli CFT073]
contig00099	2576	3376	-	chuV	100.0	99.8	NP_756180	(chuV) ATP-binding hydrophilic protein ChuV [Chu (VF0227)] [Escherichia coli CFT073]
contig00099	5514	6851	-	chuW	100.0	99.1	NP_756176	(chuW) Putative oxygen independent coproporphyrinogen III oxidase [Chu (VF0227)] [Escherichia coli CFT073]
contig00099	5007	5501	-	chuX	100.0	100.0	NP_756177	(chuX) putative heme-binding protein ChuX [Chu (VF0227)] [Escherichia coli CFT073]
contig00099	4384	5007	-	chuY	100.0	98.4	NP_756178	(chuY) ChuY [Chu (VF0227)] [Escherichia coli CFT073]
contig01740	686	1141	-	csgB	99.8	83.8	NP_460114	(csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig01814	618	1180	+	csgD	86.5	80.5	NP_460113	(csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig01707	1	690	+	csgG	82.7	84.1	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig01985	1	690	+	csgG	82.7	83.8	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00501	3489	4235	+	entA	100.0	95.7	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00502	3489	4235	+	entA	100.0	98.4	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00501	2632	3489	+	entB	100.0	98.0	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00502	2632	3489	+	entB	100.0	99.2	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00501	1	998	+	entC	84.0	97.6	NP_752611	(entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00502	1	998	+	entC	84.0	99.6	NP_752611	(entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00727	310	971	+	entD	85.9	92.8	NP_752599	(entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig01613	105	875	-	entD	100.0	95.2	NP_752599	(entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00501	1008	2618	+	entE	100.0	95.5	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00502	1008	2618	+	entE	100.0	99.1	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00063	3351	7204	+	entF	99.3	95.7	NP_752604	(entF) enterobactin synthase multienzyme complex component ATP-dependent [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00063	11494	12744	+	entS	100.0	95.4	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00230	5881	7131	+	entS	100.0	98.8	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00742	928	2827	+	espL1	100.0	97.6	NP_288154	(espL1) Type III secretion system effector espL1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00029	9625	11811	+	espL4	100.0	97.3	NP_290644	(espL4) Type III secretion system effector EspL4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00209	5270	6323	+	espR1	83.7	93.8	NP_287686	(espR1) Type III secretion system effector espR1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00243	904	2325	+	espX1	100.0	95.2	NP_285716	(espX1) Type III secretion system effector EspX1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00730	1207	2499	+	espX5	100.0	97.1	NP_290699	(espX5) Type III secretion system effector EspX5 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00746	1257	2053	+	espY1	99.9	88.8	NP_285753	(espY1) Type III secretion system effector EspY1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00031	2476	6724	-	fdeC	99.9	94.2	YP_002390132	(fdeC) adhesin FdeC [FdeC (VF0506)] [Escherichia coli O45:K1:H7 str. S88]
contig00063	12748	13704	-	fepB	100.0	97.5	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00230	7135	8000	-	fepB	90.5	99.8	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00063	8578	9393	-	fepC	100.0	97.3	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00230	2965	3780	-	fepC	100.0	99.4	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00063	10379	11395	-	fepD	100.0	96.1	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00230	4766	5782	-	fepD	100.0	99.5	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00063	9390	10382	-	fepG	100.0	94.1	NP_752607	(fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00230	3777	4769	-	fepG	100.0	99.8	NP_752607	(fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00063	1931	3133	+	fes	100.0	96.7	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00462	1931	3133	+	fes	100.0	99.8	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00194	7831	8436	-	fimA	100.0	92.2	NP_757241	(fimA) Type-1 fimbrial protein A chain precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00920	940	1542	+	fimB	100.0	98.2	NP_757239	(fimB) Type 1 fimbriae Regulatory protein fimB [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00194	6465	7190	-	fimC	100.0	98.5	NP_757243	(fimC) Chaperone protein fimC precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00194	3762	6398	-	fimD	100.0	98.3	NP_757244	(fimD) Outer membrane usher protein fimD precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00920	2020	2616	+	fimE	100.0	98.7	NP_757240	(fimE) Type 1 fimbriae Regulatory protein fimE [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00194	3222	3755	-	fimF	100.0	97.4	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00194	2706	3209	-	fimG	100.0	98.0	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00194	1784	2695	-	fimH	100.0	97.2	NP_757248	(fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00194	7227	7766	-	fimI	100.0	98.3	NP_757242	(fimI) Fimbrin-like protein fimI precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00005	26915	28936	+	fyuA	100.0	100.0	NP_405467	(fyuA) pesticin/yersiniabactin receptor protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00033	14378	15208	-	gspC	100.0	93.9	YP_404599	(gspC) general secretion pathway protein C [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00033	12288	14138	-	gspD	100.0	96.1	YP_404600	(gspD) general secretion pathway protein D [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00033	10795	12288	-	gspE	100.0	94.9	YP_404601	(gspE) general secretion pathway protein E [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00033	9596	10795	-	gspF	100.0	94.2	YP_404602	(gspF) general secretion pathway protein F [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00033	9100	9555	-	gspG	100.0	96.0	YP_404603	(gspG) general secretion pathway protein G [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00033	8533	9063	-	gspH	100.0	94.7	YP_404604	(gspH) general secretion pathway protein H [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00033	8165	8536	-	gspI	100.0	92.2	YP_404605	(gspI) general secretion pathway protein I [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00033	7563	8132	-	gspJ	100.0	94.4	YP_404606	(gspJ) general secretion pathway protein J [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00033	6589	7566	-	gspK	100.0	96.6	YP_404607	(gspK) general secretion pathway protein K [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00033	5414	6274	-	gspL	100.0	94.8	YP_404608	(gspL) general secretion pathway protein L [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00033	4877	5298	-	gspM	99.8	93.6	YP_404609	(gspM) general secretion pathway protein M [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00005	13815	23306	+	irp1	100.0	99.3	NP_405471	(irp1) yersiniabactin biosynthetic protein Irp1 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00005	7621	13725	+	irp2	100.0	98.9	NP_405472	(irp2) yersiniabactin biosynthetic protein Irp2 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00111	1259	2596	+	iucD	100.0	99.9	NP_755499	(iucD) L-lysine 6-monooxygenase IucD [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00152	1259	2580	+	iucD	98.8	96.3	NP_755499	(iucD) L-lysine 6-monooxygenase IucD [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00111	2518	4797	+	iutA	100.0	99.7	NP_755498	(iutA) ferric aerobactin receptor precusor IutA [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00152	2518	4819	+	iutA	100.0	88.4	NP_755498	(iutA) ferric aerobactin receptor precusor IutA [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00162	4502	6178	-	kpsD	100.0	99.0	AAA21682	(kpsD) KpsD [K1 capsule (VF0239)] [Escherichia coli O18:K1:H7 str. RS218]
contig00033	3041	3817	-	kpsM	100.0	99.9	AAA24046	(kpsM) KpsM [K1 capsule (VF0239)] [Escherichia coli O18:K1:H7 str. RS218]
contig00033	2385	3044	-	kpsT	100.0	100.0	AAA24047	(kpsT) KpsT [K1 capsule (VF0239)] [Escherichia coli O18:K1:H7 str. RS218]
contig00334	1178	2218	-	ompA	100.0	98.1	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig02092	1	894	+	ompA	85.9	99.4	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00211	747	1060	-	papB	99.7	98.4		(papB) regulatory protein PapB [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig00211	1465	1698	+	papI	100.0	94.9	NP_755468	(papI) regulatory protein PapI [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig01745	255	806	+	papX	100.0	97.5	NP_755457	(papX) PapX protein regulates flagellum synthesis to repress motility [P fimbriae (CVF425)] [Escherichia coli CFT073]
contig00152	5754	9654	+	sat	100.0	99.5	NP_755494	(sat) Aecreted auto transpoter toxin [Sat (VF0231)] [Escherichia coli CFT073]
contig00131	8438	9576	+	senB	99.9	99.7	YP_406304	(senB) enterotoxin [ShET2 (VF0258)] [Shigella flexneri 2a str. 301]
contig00110	354	4485	+	vat	100.0	99.7	NP_752330	(vat) Haemoglobin protease [Tsh (VF0233)] [Escherichia coli CFT073]
contig00031	15831	16584	+	yagV/ecpE	99.7	97.1	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00509	625	1378	+	yagV/ecpE	99.7	98.4	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00031	14264	15907	+	yagW/ecpD	100.0	99.1	NP_286007	(yagW/ecpD) polymerized tip adhesin of ECP fibers [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00031	11749	14274	+	yagX/ecpC	100.0	98.8	NP_286008	(yagX/ecpC) E. coli common pilus usher EcpC [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00875	1	2293	+	yagX/ecpC	90.8	97.4	NP_286008	(yagX/ecpC) E. coli common pilus usher EcpC [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00031	11055	11723	+	yagY/ecpB	100.0	98.1	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00065	13581	14188	+	yagY/ecpB	90.9	97.9	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00031	10410	10997	+	yagZ/ecpA	100.0	99.2	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00065	12937	13524	+	yagZ/ecpA	100.0	98.5	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00005	6471	7430	+	ybtA	100.0	99.5	NP_405473	(ybtA) transcriptional regulator YbtA [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00005	25207	26784	+	ybtE	100.0	99.8	NP_405468	(ybtE) yersiniabactin siderophore biosynthetic protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00005	4502	6304	-	ybtP	100.0	99.6	NP_405474	(ybtP) lipoprotein inner membrane ABC-transporter [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00005	2713	4515	-	ybtQ	100.0	99.8	NP_405475	(ybtQ) inner membrane ABC-transporter YbtQ [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00005	108	1412	-	ybtS	100.0	99.8	NP_405477	(ybtS) salicylate synthase Irp9 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00005	24400	25203	+	ybtT	100.0	99.5	NP_405469	(ybtT) yersiniabactin biosynthetic protein YbtT [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00005	23303	24403	+	ybtU	100.0	99.7	NP_405470	(ybtU) yersiniabactin biosynthetic protein YbtU [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00005	1440	2720	-	ybtX	100.0	99.6	NP_405476	(ybtX) putative signal transducer [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00031	9745	10335	+	ykgK/ecpR	100.0	97.0	NP_286011	(ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00065	12272	12862	+	ykgK/ecpR	100.0	99.3	NP_286011	(ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

ID067

Contig	Start	End	Strand	Gene	Coverage	Identity	Accession	Product
contig00075	1130	1585	-	csgB	99.8	83.6	NP_460114	(csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00075	2340	2990	+	csgD	100.0	81.3	NP_460113	(csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00075	3409	3825	+	csgF	99.0	81.2	NP_460111	(csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00075	3852	4685	+	csgG	100.0	83.5	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00016	73488	74234	-	entA	100.0	95.7	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00016	74234	75091	-	entB	100.0	98.1	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00016	76725	77912	-	entC	100.0	97.9	NP_752611	(entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00016	92556	93326	+	entD	100.0	94.3	NP_752599	(entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00016	75105	76715	-	entE	100.0	95.4	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00016	84775	88628	-	entF	99.3	95.6	NP_752604	(entF) enterobactin synthase multienzyme complex component ATP-dependent [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00016	79235	80485	-	entS	100.0	95.4	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00028	44763	45818	+	espR1	83.8	94.0	NP_287686	(espR1) Type III secretion system effector espR1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00002	202051	203471	+	espX1	99.9	95.2	NP_285716	(espX1) Type III secretion system effector EspX1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00014	56912	58491	-	espX4	99.9	93.2	NP_290672	(espX4) Type III secretion system effector EspX4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00014	26120	27412	+	espX5	100.0	95.7	NP_290699	(espX5) Type III secretion system effector EspX5 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00016	90291	92531	+	fepA	100.0	96.8	NP_752600	(fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00016	78275	79231	+	fepB	100.0	97.5	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00016	82586	83401	+	fepC	100.0	97.3	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00016	80584	81600	+	fepD	100.0	96.0	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00016	81597	82589	+	fepG	100.0	94.1	NP_752607	(fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00016	88846	90048	-	fes	100.0	96.5	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00017	91291	91824	-	fimF	100.0	97.6	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00017	90775	91278	-	fimG	100.0	97.4	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00017	89853	90764	-	fimH	100.0	97.6	NP_757248	(fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00006	82761	83291	-	gspH	100.0	97.2	YP_404604	(gspH) general secretion pathway protein H [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00006	82393	82764	-	gspI	100.0	94.9	YP_404605	(gspI) general secretion pathway protein I [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00006	81791	82360	-	gspJ	100.0	97.2	YP_404606	(gspJ) general secretion pathway protein J [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00006	80817	81794	-	gspK	100.0	98.2	YP_404607	(gspK) general secretion pathway protein K [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00006	79642	80502	-	gspL	100.0	97.1	YP_404608	(gspL) general secretion pathway protein L [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00006	79104	79526	-	gspM	100.0	94.8	YP_404609	(gspM) general secretion pathway protein M [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00076	1510	1872	+	gtrA	100.0	90.4	NP_706257	(gtrA) bactoprenol-linked glucose translocase/flippase [LPS (VF0124)] [Shigella flexneri 2a str. 301]
contig00009	103199	104239	-	ompA	100.0	98.1	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]

ID068

Contig	Start	End	Strand	Gene	Coverage	Identity	Accession	Product
contig00021	49065	50493	+	aslA	100.0	93.6	AAG10151	(aslA) putative arylsulfatase [AslA (VF0238)] [Escherichia coli O18:K1:H7 str. RS218]
contig00007	8083	8538	+	csgB	99.8	83.8	NP_460114	(csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00007	6678	7328	-	csgD	100.0	81.1	NP_460113	(csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00007	5843	6259	-	csgF	99.0	81.2	NP_460111	(csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00007	4983	5816	-	csgG	100.0	83.5	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00012	99274	100020	-	entA	100.0	95.7	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00012	100020	100877	-	entB	100.0	98.1	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00012	102511	103698	-	entC	100.0	97.9	NP_752611	(entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00012	118342	119112	+	entD	100.0	95.2	NP_752599	(entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00012	100891	102501	-	entE	100.0	95.4	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00012	110561	114414	-	entF	99.3	95.7	NP_752604	(entF) enterobactin synthase multienzyme complex component ATP-dependent [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00012	105021	106271	-	entS	100.0	95.4	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00001	251616	253515	-	espL1	100.0	97.6	NP_288154	(espL1) Type III secretion system effector espL1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00017	91936	94122	+	espL4	100.0	97.3	NP_290644	(espL4) Type III secretion system effector EspL4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00037	25267	26320	+	espR1	83.7	93.8	NP_287686	(espR1) Type III secretion system effector espR1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00001	45175	46310	+	espR4	99.6	84.5	NP_288396	(espR4) Type III secretion system effector espR4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00008	144166	145587	+	espX1	100.0	94.7	NP_285716	(espX1) Type III secretion system effector EspX1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00017	62140	63720	-	espX4	99.9	93.3	NP_290672	(espX4) Type III secretion system effector EspX4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00017	31350	32641	+	espX5	99.9	97.0	NP_290699	(espX5) Type III secretion system effector EspX5 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00008	105277	106058	-	espY1	99.9	90.4	NP_285753	(espY1) Type III secretion system effector EspY1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00012	116077	118317	+	fepA	100.0	96.7	NP_752600	(fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00012	104061	105017	+	fepB	100.0	97.5	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00012	108372	109187	+	fepC	100.0	97.3	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00012	106370	107386	+	fepD	100.0	96.1	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00012	107383	108375	+	fepG	100.0	94.1	NP_752607	(fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00012	114632	115834	-	fes	100.0	96.7	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00006	103766	104806	-	ompA	100.0	98.0	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00031	5924	6677	+	yagV/ecpE	99.7	97.1	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00031	4357	6000	+	yagW/ecpD	100.0	99.1	NP_286007	(yagW/ecpD) polymerized tip adhesin of ECP fibers [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00031	1842	4367	+	yagX/ecpC	100.0	98.8	NP_286008	(yagX/ecpC) E. coli common pilus usher EcpC [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00031	1148	1816	+	yagY/ecpB	100.0	98.1	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00031	503	1090	+	yagZ/ecpA	100.0	99.2	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

ID073I

Contig	Start	End	Strand	Gene	Coverage	Identity	Accession	Product
contig00056	14045	14500	-	csgB	99.8	83.6	NP_460114	(csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00056	15255	15905	+	csgD	100.0	81.3	NP_460113	(csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00056	16324	16740	+	csgF	99.0	81.2	NP_460111	(csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00056	16767	17600	+	csgG	100.0	83.5	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00015	73616	74362	-	entA	100.0	95.7	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00015	74362	75219	-	entB	100.0	98.1	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00015	76853	78040	-	entC	100.0	97.9	NP_752611	(entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00015	92684	93454	+	entD	100.0	94.2	NP_752599	(entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00015	75233	76843	-	entE	100.0	95.4	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00015	84903	88756	-	entF	99.3	95.6	NP_752604	(entF) enterobactin synthase multienzyme complex component ATP-dependent [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00015	79363	80613	-	entS	100.0	95.4	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00011	70946	72001	+	espR1	83.8	94.0	NP_287686	(espR1) Type III secretion system effector espR1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00003	201882	203302	+	espX1	99.9	95.2	NP_285716	(espX1) Type III secretion system effector EspX1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00014	56912	58492	-	espX4	99.9	93.3	NP_290672	(espX4) Type III secretion system effector EspX4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00014	26120	27412	+	espX5	100.0	95.6	NP_290699	(espX5) Type III secretion system effector EspX5 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00015	90419	92659	+	fepA	100.0	96.8	NP_752600	(fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00015	78403	79359	+	fepB	100.0	97.5	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00015	82714	83529	+	fepC	100.0	97.3	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00015	80712	81728	+	fepD	100.0	96.1	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00015	81725	82717	+	fepG	100.0	94.1	NP_752607	(fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00015	88974	90176	-	fes	100.0	96.6	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00016	89982	90515	-	fimF	100.0	97.8	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00016	89466	89969	-	fimG	100.0	97.4	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00016	88544	89455	-	fimH	100.0	97.6	NP_757248	(fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00024	16594	17124	-	gspH	100.0	97.2	YP_404604	(gspH) general secretion pathway protein H [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00024	16226	16597	-	gspI	100.0	94.9	YP_404605	(gspI) general secretion pathway protein I [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00024	15624	16193	-	gspJ	100.0	97.2	YP_404606	(gspJ) general secretion pathway protein J [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00024	14650	15627	-	gspK	100.0	98.2	YP_404607	(gspK) general secretion pathway protein K [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00024	13475	14335	-	gspL	100.0	97.1	YP_404608	(gspL) general secretion pathway protein L [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00024	12937	13359	-	gspM	100.0	94.8	YP_404609	(gspM) general secretion pathway protein M [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00002	73598	74638	+	ompA	100.0	98.1	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]

ID077

Contig	Start	End	Strand	Gene	Coverage	Identity	Accession	Product
contig00003	178149	178604	+	csgB	99.8	84.0	NP_460114	(csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00003	176745	177395	-	csgD	100.0	81.1	NP_460113	(csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00003	175910	176326	-	csgF	99.0	81.2	NP_460111	(csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00003	175050	175883	-	csgG	100.0	83.1	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00006	99458	100204	-	entA	100.0	96.0	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00006	100204	101061	-	entB	100.0	97.9	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00006	102695	103882	-	entC	100.0	97.5	NP_752611	(entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00006	118526	119296	+	entD	100.0	94.0	NP_752599	(entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00006	101075	102685	-	entE	100.0	95.8	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00006	110769	114598	-	entF	98.7	95.4	NP_752604	(entF) enterobactin synthase multienzyme complex component ATP-dependent [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00006	105205	106455	-	entS	100.0	95.6	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00002	94169	96037	+	espL1	98.4	95.3	NP_288154	(espL1) Type III secretion system effector espL1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00036	24866	25921	+	espR1	83.8	94.2	NP_287686	(espR1) Type III secretion system effector espR1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00011	142352	143772	+	espX1	99.9	94.7	NP_285716	(espX1) Type III secretion system effector EspX1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00019	55500	57080	-	espX4	99.9	93.1	NP_290672	(espX4) Type III secretion system effector EspX4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00019	24689	25981	+	espX5	100.0	95.7	NP_290699	(espX5) Type III secretion system effector EspX5 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00015	43044	47285	-	fdeC	99.8	92.4	YP_002390132	(fdeC) adhesin FdeC [FdeC (VF0506)] [Escherichia coli O45:K1:H7 str. S88]
contig00006	116261	118501	+	fepA	100.0	96.8	NP_752600	(fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00006	104245	105201	+	fepB	100.0	97.4	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00006	108556	109371	+	fepC	100.0	97.3	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00006	106554	107570	+	fepD	100.0	96.0	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00006	107567	108559	+	fepG	100.0	94.0	NP_752607	(fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00006	114816	116018	-	fes	100.0	96.8	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00016	107592	108196	-	fimA	99.8	90.6	NP_757241	(fimA) Type-1 fimbrial protein A chain precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00037	39377	39979	+	fimB	100.0	97.8	NP_757239	(fimB) Type 1 fimbriae Regulatory protein fimB [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00016	106220	106945	-	fimC	100.0	98.6	NP_757243	(fimC) Chaperone protein fimC precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00016	103517	106153	-	fimD	100.0	98.7	NP_757244	(fimD) Outer membrane usher protein fimD precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00037	40457	41053	+	fimE	100.0	99.2	NP_757240	(fimE) Type 1 fimbriae Regulatory protein fimE [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00016	102977	103510	-	fimF	100.0	96.6	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00016	102461	102964	-	fimG	100.0	97.8	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00016	101539	102450	-	fimH	100.0	97.7	NP_757248	(fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00016	106988	107527	-	fimI	100.0	99.1	NP_757242	(fimI) Fimbrin-like protein fimI precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00001	319119	319949	-	gspC	100.0	95.1	YP_404599	(gspC) general secretion pathway protein C [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	317029	318879	-	gspD	100.0	97.0	YP_404600	(gspD) general secretion pathway protein D [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	315536	317029	-	gspE	100.0	97.1	YP_404601	(gspE) general secretion pathway protein E [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	314337	315536	-	gspF	100.0	96.2	YP_404602	(gspF) general secretion pathway protein F [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	313841	314296	-	gspG	100.0	95.6	YP_404603	(gspG) general secretion pathway protein G [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	313274	313804	-	gspH	100.0	96.0	YP_404604	(gspH) general secretion pathway protein H [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	312906	313277	-	gspI	100.0	95.2	YP_404605	(gspI) general secretion pathway protein I [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	312304	312873	-	gspJ	100.0	97.2	YP_404606	(gspJ) general secretion pathway protein J [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	311330	312307	-	gspK	100.0	96.1	YP_404607	(gspK) general secretion pathway protein K [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	310155	311015	-	gspL	100.0	97.6	YP_404608	(gspL) general secretion pathway protein L [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	309617	310039	-	gspM	100.0	94.1	YP_404609	(gspM) general secretion pathway protein M [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00003	104182	105234	-	ompA	100.0	94.3	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00015	56391	57144	+	yagV/ecpE	99.7	96.8	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00015	54824	56467	+	yagW/ecpD	100.0	98.5	NP_286007	(yagW/ecpD) polymerized tip adhesin of ECP fibers [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00015	52309	54834	+	yagX/ecpC	100.0	98.7	NP_286008	(yagX/ecpC) E. coli common pilus usher EcpC [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00015	51615	52283	+	yagY/ecpB	100.0	98.7	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00015	50970	51557	+	yagZ/ecpA	100.0	99.3	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00015	50305	50895	+	ykgK/ecpR	100.0	97.6	NP_286011	(ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

ID081I

Contig	Start	End	Strand	Gene	Coverage	Identity	Accession	Product
contig00073	1312	1767	-	csgB	99.8	83.6	NP_460114	(csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00073	2522	3172	+	csgD	100.0	81.3	NP_460113	(csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00073	3591	4007	+	csgF	99.0	81.2	NP_460111	(csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00073	4034	4867	+	csgG	100.0	83.5	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00002	188935	189681	-	entA	100.0	96.7	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00002	189681	190538	-	entB	100.0	98.1	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00002	192172	193359	-	entC	100.0	97.9	NP_752611	(entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00002	208003	208773	+	entD	100.0	95.2	NP_752599	(entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00002	190552	192162	-	entE	100.0	95.5	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00002	200222	204075	-	entF	99.3	95.7	NP_752604	(entF) enterobactin synthase multienzyme complex component ATP-dependent [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00002	194682	195932	-	entS	100.0	95.7	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00007	53659	55558	-	espL1	100.0	97.6	NP_288154	(espL1) Type III secretion system effector espL1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00020	51792	53372	-	espX4	99.9	93.2	NP_290672	(espX4) Type III secretion system effector EspX4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00020	20999	22291	+	espX5	100.0	98.1	NP_290699	(espX5) Type III secretion system effector EspX5 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00038	3583	7831	+	fdeC	99.9	94.2	YP_002390132	(fdeC) adhesin FdeC [FdeC (VF0506)] [Escherichia coli O45:K1:H7 str. S88]
contig00002	205738	207978	+	fepA	100.0	96.8	NP_752600	(fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00002	193722	194678	+	fepB	100.0	97.5	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00002	198033	198848	+	fepC	100.0	97.3	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00002	196031	197047	+	fepD	100.0	95.6	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00002	197044	198036	+	fepG	100.0	94.8	NP_752607	(fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00002	204293	205495	-	fes	100.0	96.6	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00054	19054	19965	-	fimH	100.0	97.2	NP_757248	(fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00014	73515	75536	+	fyuA	100.0	100.0	NP_405467	(fyuA) pesticin/yersiniabactin receptor protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00001	209199	210029	-	gspC	100.0	95.3	YP_404599	(gspC) general secretion pathway protein C [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	207109	208959	-	gspD	100.0	97.1	YP_404600	(gspD) general secretion pathway protein D [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	205692	207109	-	gspE	94.9	97.1	YP_404601	(gspE) general secretion pathway protein E [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00014	60415	69906	+	irp1	100.0	99.9	NP_405471	(irp1) yersiniabactin biosynthetic protein Irp1 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00014	54220	60327	+	irp2	100.0	99.8	NP_405472	(irp2) yersiniabactin biosynthetic protein Irp2 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00009	124013	125053	-	ompA	100.0	98.1	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00014	53070	54029	+	ybtA	100.0	99.8	NP_405473	(ybtA) transcriptional regulator YbtA [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00014	71807	73384	+	ybtE	100.0	99.8	NP_405468	(ybtE) yersiniabactin siderophore biosynthetic protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00014	51101	52903	-	ybtP	100.0	99.7	NP_405474	(ybtP) lipoprotein inner membrane ABC-transporter [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00014	49312	51114	-	ybtQ	100.0	99.9	NP_405475	(ybtQ) inner membrane ABC-transporter YbtQ [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00014	46707	48011	-	ybtS	100.0	97.6	NP_405477	(ybtS) salicylate synthase Irp9 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00014	71000	71803	+	ybtT	100.0	99.8	NP_405469	(ybtT) yersiniabactin biosynthetic protein YbtT [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00014	69903	71003	+	ybtU	100.0	99.7	NP_405470	(ybtU) yersiniabactin biosynthetic protein YbtU [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00014	48039	49319	-	ybtX	100.0	97.7	NP_405476	(ybtX) putative signal transducer [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00038	1	563	-	ykgK/ecpR	95.3	97.0	NP_286011	(ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

ID086II

Contig	Start	End	Strand	Gene	Coverage	Identity	Accession	Product
contig00022	73361	73666	-	afaA	100.0	100.0	CAW30797	(afaA) fimbrial major subunit AfaA [Afimbrial adhesin AFA-I mannose-resistant adhesin (AI010)] [Escherichia coli O25b:H4 str. FV9863]
contig00022	72326	73070	-	afaB-I	100.0	99.6	CAW30798	(afaB-I) chaperone AfaB [Afimbrial adhesin AFA-I mannose-resistant adhesin (AI010)] [Escherichia coli O25b:H4 str. FV9863]
contig00022	69651	72233	-	afaC-I	100.0	99.9	CAW30799	(afaC-I) usher AfaC [Afimbrial adhesin AFA-I mannose-resistant adhesin (AI010)] [Escherichia coli O25b:H4 str. FV9863]
contig00022	69192	69635	-	afaD	100.0	100.0	CAW30800	(afaD) AfaD [Afimbrial adhesin AFA-I mannose-resistant adhesin (AI010)] [Escherichia coli O25b:H4 str. FV9863]
contig00022	67954	68439	-	afaE-I	100.0	99.8	CAW30801	(afaE-I) AFA-I adhesin [Afa/Dr family (VF0212)] [Escherichia coli O25b:H4 str. FV9863]
contig00018	71053	72481	+	aslA	100.0	98.2	AAG10151	(aslA) putative arylsulfatase [AslA (VF0238)] [Escherichia coli O18:K1:H7 str. RS218]
contig00029	16900	18846	+	chuA	100.0	99.5	NP_756170	(chuA) Outer membrane heme/hemoglobin receptor ChuA [Chu (VF0227)] [Escherichia coli CFT073]
contig00029	18895	19923	+	chuS	100.0	99.0	NP_756169	(chuS) heme oxygenase ChuS [Chu (VF0227)] [Escherichia coli CFT073]
contig00029	15266	16258	-	chuT	100.0	99.8	NP_756175	(chuT) periplasmic heme-binding protein ChuT [Chu (VF0227)] [Escherichia coli CFT073]
contig00029	11738	12730	-	chuU	100.0	99.5	NP_756179	(chuU) heme permease protein ChuU [Chu (VF0227)] [Escherichia coli CFT073]
contig00029	10971	11771	-	chuV	100.0	99.8	NP_756180	(chuV) ATP-binding hydrophilic protein ChuV [Chu (VF0227)] [Escherichia coli CFT073]
contig00029	13909	15246	-	chuW	100.0	98.9	NP_756176	(chuW) Putative oxygen independent coproporphyrinogen III oxidase [Chu (VF0227)] [Escherichia coli CFT073]
contig00029	13402	13896	-	chuX	100.0	100.0	NP_756177	(chuX) putative heme-binding protein ChuX [Chu (VF0227)] [Escherichia coli CFT073]
contig00029	12779	13402	-	chuY	100.0	98.2	NP_756178	(chuY) ChuY [Chu (VF0227)] [Escherichia coli CFT073]
contig00010	102918	103373	-	csgB	99.8	83.8	NP_460114	(csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00010	104126	104776	+	csgD	100.0	81.6	NP_460113	(csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00010	105195	105611	+	csgF	99.0	80.8	NP_460111	(csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00010	105638	106471	+	csgG	100.0	83.2	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00022	74584	74811	+	daaF	100.0	100.0	AAA23662	(daaF) DaaF protein [F1845 fimbrial adhesin (AI016)] [Escherichia coli str. C1845]
contig00022	68641	68814	-	draP	100.0	98.8	AAK16479	(draP) DraP [Dr adhesins (VF0223)] [Escherichia coli O75:K5:H- str. IH11128]
contig00001	281532	282278	-	entA	100.0	98.1	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00001	282278	283135	-	entB	100.0	99.4	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00001	284769	285956	-	entC	100.0	98.7	NP_752611	(entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00001	300445	301106	+	entD	85.9	96.7	NP_752599	(entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00001	283149	284759	-	entE	100.0	98.9	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00001	292636	296517	-	entF	100.0	98.2	NP_752604	(entF) enterobactin synthase multienzyme complex component ATP-dependent [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00001	287093	288343	-	entS	100.0	97.4	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00001	573409	577656	-	fdeC	99.9	97.4	YP_002390132	(fdeC) adhesin FdeC [FdeC (VF0506)] [Escherichia coli O45:K1:H7 str. S88]
contig00001	298180	300420	+	fepA	100.0	98.9	NP_752600	(fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00001	286133	287089	+	fepB	100.0	98.4	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00001	290444	291259	+	fepC	100.0	99.1	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00001	288442	289458	+	fepD	100.0	97.8	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00001	289455	290447	+	fepG	100.0	97.9	NP_752607	(fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00001	296735	297937	-	fes	100.0	99.0	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00003	331496	332100	-	fimA	99.8	90.8	NP_757241	(fimA) Type-1 fimbrial protein A chain precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00003	330130	330855	-	fimC	100.0	98.9	NP_757243	(fimC) Chaperone protein fimC precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00003	327427	330063	-	fimD	100.0	98.5	NP_757244	(fimD) Outer membrane usher protein fimD precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00003	332523	333119	-	fimE	100.0	98.8	NP_757240	(fimE) Type 1 fimbriae Regulatory protein fimE [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00003	326887	327420	-	fimF	100.0	96.6	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00003	326371	326874	-	fimG	100.0	98.2	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00003	325449	326360	-	fimH	100.0	97.5	NP_757248	(fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00003	330892	331431	-	fimI	100.0	98.5	NP_757242	(fimI) Fimbrin-like protein fimI precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00028	31110	33131	+	fyuA	100.0	99.8	NP_405467	(fyuA) pesticin/yersiniabactin receptor protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00007	167409	168239	+	gspC	100.0	93.9	YP_404599	(gspC) general secretion pathway protein C [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00007	168479	170329	+	gspD	100.0	96.1	YP_404600	(gspD) general secretion pathway protein D [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00007	170329	171822	+	gspE	100.0	95.0	YP_404601	(gspE) general secretion pathway protein E [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00007	171822	173021	+	gspF	100.0	94.2	YP_404602	(gspF) general secretion pathway protein F [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00007	173062	173517	+	gspG	100.0	96.0	YP_404603	(gspG) general secretion pathway protein G [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00007	173554	174084	+	gspH	100.0	94.7	YP_404604	(gspH) general secretion pathway protein H [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00007	174081	174452	+	gspI	100.0	92.2	YP_404605	(gspI) general secretion pathway protein I [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00007	174485	175054	+	gspJ	100.0	94.4	YP_404606	(gspJ) general secretion pathway protein J [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00007	175051	176028	+	gspK	100.0	96.6	YP_404607	(gspK) general secretion pathway protein K [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00007	176343	177203	+	gspL	100.0	94.8	YP_404608	(gspL) general secretion pathway protein L [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00007	177319	177740	+	gspM	99.8	92.9	YP_404609	(gspM) general secretion pathway protein M [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00028	18010	27501	+	irp1	100.0	99.8	NP_405471	(irp1) yersiniabactin biosynthetic protein Irp1 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00028	11815	17922	+	irp2	100.0	99.4	NP_405472	(irp2) yersiniabactin biosynthetic protein Irp2 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00037	8835	10616	+	iucA	100.0	99.8	NP_709454	(iucA) aerobactin synthesis protein IucA [Aerobactin (VF0123)] [Shigella flexneri 2a str. 301]
contig00037	10617	11564	+	iucB	100.0	99.8	NP_709455	(iucB) aerobactin synthesis protein IucB [Aerobactin (VF0123)] [Shigella flexneri 2a str. 301]
contig00037	11564	13306	+	iucC	100.0	98.2	NP_755500	(iucC) aerobactin siderophore biosynthesis protein IucC [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00037	13303	14624	+	iucD	98.8	96.3	NP_755499	(iucD) L-lysine 6-monooxygenase IucD [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00037	14562	16863	+	iutA	100.0	88.4	NP_755498	(iutA) ferric aerobactin receptor precusor IutA [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00007	192461	194137	-	kpsD	100.0	98.3	AAA21682	(kpsD) KpsD [K1 capsule (VF0239)] [Escherichia coli O18:K1:H7 str. RS218]
contig00007	178799	179575	+	kpsM	100.0	94.7	AAA24046	(kpsM) KpsM [K1 capsule (VF0239)] [Escherichia coli O18:K1:H7 str. RS218]
contig00015	1055	2107	+	ompA	100.0	95.8	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00037	749	1062	-	papB	99.7	98.4		(papB) regulatory protein PapB [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig00037	1467	1700	+	papI	100.0	94.9	NP_755468	(papI) regulatory protein PapI [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig00073	256	807	+	papX	100.0	97.6	NP_755457	(papX) PapX protein regulates flagellum synthesis to repress motility [P fimbriae (CVF425)] [Escherichia coli CFT073]
contig00037	17795	21694	+	sat	100.0	99.6	NP_755494	(sat) Aecreted auto transpoter toxin [Sat (VF0231)] [Escherichia coli CFT073]
contig00048	8392	9530	+	senB	99.9	99.7	YP_406304	(senB) enterotoxin [ShET2 (VF0258)] [Shigella flexneri 2a str. 301]
contig00001	592994	593747	+	yagV/ecpE	99.7	98.0	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00001	591427	593070	+	yagW/ecpD	100.0	99.2	NP_286007	(yagW/ecpD) polymerized tip adhesin of ECP fibers [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00001	588912	591437	+	yagX/ecpC	100.0	97.6	NP_286008	(yagX/ecpC) E. coli common pilus usher EcpC [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00001	588218	588886	+	yagY/ecpB	100.0	98.1	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00001	587574	588161	+	yagZ/ecpA	100.0	98.5	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00028	10665	11624	+	ybtA	100.0	99.3	NP_405473	(ybtA) transcriptional regulator YbtA [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00028	29402	30979	+	ybtE	100.0	99.8	NP_405468	(ybtE) yersiniabactin siderophore biosynthetic protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00028	8696	10498	-	ybtP	100.0	99.6	NP_405474	(ybtP) lipoprotein inner membrane ABC-transporter [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00028	6907	8709	-	ybtQ	100.0	99.6	NP_405475	(ybtQ) inner membrane ABC-transporter YbtQ [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00028	4302	5606	-	ybtS	100.0	99.8	NP_405477	(ybtS) salicylate synthase Irp9 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00028	28595	29398	+	ybtT	100.0	99.6	NP_405469	(ybtT) yersiniabactin biosynthetic protein YbtT [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00028	27498	28598	+	ybtU	100.0	99.7	NP_405470	(ybtU) yersiniabactin biosynthetic protein YbtU [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00028	5634	6914	-	ybtX	100.0	99.7	NP_405476	(ybtX) putative signal transducer [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00001	586909	587499	+	ykgK/ecpR	100.0	99.5	NP_286011	(ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

ID088

Contig	Start	End	Strand	Gene	Coverage	Identity	Accession	Product
contig00020	49279	50707	+	aslA	100.0	93.6	AAG10151	(aslA) putative arylsulfatase [AslA (VF0238)] [Escherichia coli O18:K1:H7 str. RS218]
contig00032	40480	40935	-	csgB	99.8	83.8	NP_460114	(csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00032	41690	42340	+	csgD	100.0	81.1	NP_460113	(csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00032	42759	43175	+	csgF	99.0	81.2	NP_460111	(csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00032	43202	44035	+	csgG	100.0	83.3	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00011	99570	100316	-	entA	100.0	95.7	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00011	100316	101173	-	entB	100.0	98.0	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00011	102807	103994	-	entC	100.0	97.9	NP_752611	(entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00011	118638	119408	+	entD	100.0	95.2	NP_752599	(entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00011	101187	102797	-	entE	100.0	95.5	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00011	110857	114710	-	entF	99.3	95.7	NP_752604	(entF) enterobactin synthase multienzyme complex component ATP-dependent [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00011	105317	106567	-	entS	100.0	95.4	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00048	18427	20325	+	espL1	100.0	97.6	NP_288154	(espL1) Type III secretion system effector espL1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00047	19357	21543	+	espL4	100.0	97.3	NP_290644	(espL4) Type III secretion system effector EspL4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00038	25267	26320	+	espR1	83.7	93.8	NP_287686	(espR1) Type III secretion system effector espR1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00014	48323	49458	-	espR4	99.6	84.4	NP_288396	(espR4) Type III secretion system effector espR4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00006	203426	204847	+	espX1	100.0	95.2	NP_285716	(espX1) Type III secretion system effector EspX1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00008	164241	165821	-	espX4	99.9	93.3	NP_290672	(espX4) Type III secretion system effector EspX4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00008	133450	134742	+	espX5	100.0	97.1	NP_290699	(espX5) Type III secretion system effector EspX5 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00006	164472	165283	-	espY1	99.9	87.0	NP_285753	(espY1) Type III secretion system effector EspY1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00002	204341	208589	-	fdeC	99.9	94.2	YP_002390132	(fdeC) adhesin FdeC [FdeC (VF0506)] [Escherichia coli O45:K1:H7 str. S88]
contig00011	116373	118613	+	fepA	100.0	96.7	NP_752600	(fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00011	104357	105313	+	fepB	100.0	97.5	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00011	108668	109483	+	fepC	100.0	97.3	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00011	106666	107682	+	fepD	100.0	96.1	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00011	107679	108671	+	fepG	100.0	94.1	NP_752607	(fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00011	114928	116130	-	fes	100.0	96.7	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00024	39622	41643	-	fyuA	100.0	100.0	NP_405467	(fyuA) pesticin/yersiniabactin receptor protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00024	45252	54743	-	irp1	100.0	99.8	NP_405471	(irp1) yersiniabactin biosynthetic protein Irp1 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00024	54831	60938	-	irp2	100.0	99.8	NP_405472	(irp2) yersiniabactin biosynthetic protein Irp2 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00053	7015	8802	+	iucA	100.0	94.2	NP_755502	(iucA) aerobactin siderophore biosynthesis protein IucD [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00053	8803	9750	+	iucB	100.0	95.6	NP_755501	(iucB) aerobactin siderophore biosynthesis protein IucB [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00053	9750	11492	+	iucC	100.0	96.0	NP_755500	(iucC) aerobactin siderophore biosynthesis protein IucC [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00053	11489	12810	+	iucD	98.8	96.3	NP_755499	(iucD) L-lysine 6-monooxygenase IucD [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00053	12748	15049	+	iutA	100.0	88.4	NP_755498	(iutA) ferric aerobactin receptor precusor IutA [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00001	286346	287386	-	ompA	100.0	98.1	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00002	217696	218449	+	yagV/ecpE	99.7	97.1	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00002	216129	217772	+	yagW/ecpD	100.0	99.1	NP_286007	(yagW/ecpD) polymerized tip adhesin of ECP fibers [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00002	213614	216139	+	yagX/ecpC	100.0	98.8	NP_286008	(yagX/ecpC) E. coli common pilus usher EcpC [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00002	212920	213588	+	yagY/ecpB	100.0	98.1	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00002	212275	212862	+	yagZ/ecpA	100.0	99.2	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00024	61129	62088	-	ybtA	100.0	99.9	NP_405473	(ybtA) transcriptional regulator YbtA [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00024	41774	43351	-	ybtE	100.0	99.8	NP_405468	(ybtE) yersiniabactin siderophore biosynthetic protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00024	62255	64057	+	ybtP	100.0	99.6	NP_405474	(ybtP) lipoprotein inner membrane ABC-transporter [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00024	64044	65846	+	ybtQ	100.0	99.8	NP_405475	(ybtQ) inner membrane ABC-transporter YbtQ [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00024	67147	68451	+	ybtS	100.0	97.6	NP_405477	(ybtS) salicylate synthase Irp9 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00024	43355	44158	-	ybtT	100.0	99.8	NP_405469	(ybtT) yersiniabactin biosynthetic protein YbtT [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00024	44155	45255	-	ybtU	100.0	99.7	NP_405470	(ybtU) yersiniabactin biosynthetic protein YbtU [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00024	65839	67119	+	ybtX	100.0	97.7	NP_405476	(ybtX) putative signal transducer [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00002	211610	212200	+	ykgK/ecpR	100.0	97.0	NP_286011	(ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

ID092

Contig	Start	End	Strand	Gene	Coverage	Identity	Accession	Product
contig01686	962	1267	-	afaA	100.0	99.7	CAW30797	(afaA) fimbrial major subunit AfaA [Afimbrial adhesin AFA-I mannose-resistant adhesin (AI010)] [Escherichia coli O25b:H4 str. FV9863]
contig01686	1	692	-	afaB-I	93.0	100.0	CAW30798	(afaB-I) chaperone AfaB [Afimbrial adhesin AFA-I mannose-resistant adhesin (AI010)] [Escherichia coli O25b:H4 str. FV9863]
contig00659	1597	4179	-	afaC-I	100.0	99.2	CAW30799	(afaC-I) usher AfaC [Afimbrial adhesin AFA-I mannose-resistant adhesin (AI010)] [Escherichia coli O25b:H4 str. FV9863]
contig00659	1	391	-	afaE-V	81.0	98.2	CAA62863	(afaE-V) AfaE-V adhesin [Afimbrial adhesin AFA-V (AI013)] [Escherichia coli str. AL 851]
contig00811	409	1837	+	aslA	100.0	97.4	AAG10151	(aslA) putative arylsulfatase [AslA (VF0238)] [Escherichia coli O18:K1:H7 str. RS218]
contig00207	464	1492	-	chuS	100.0	98.0	NP_756169	(chuS) heme oxygenase ChuS [Chu (VF0227)] [Escherichia coli CFT073]
contig00207	4129	5121	+	chuT	100.0	99.4	NP_756175	(chuT) periplasmic heme-binding protein ChuT [Chu (VF0227)] [Escherichia coli CFT073]
contig00207	7657	8649	+	chuU	100.0	99.1	NP_756179	(chuU) heme permease protein ChuU [Chu (VF0227)] [Escherichia coli CFT073]
contig00207	8616	9416	+	chuV	100.0	98.4	NP_756180	(chuV) ATP-binding hydrophilic protein ChuV [Chu (VF0227)] [Escherichia coli CFT073]
contig00207	5141	6478	+	chuW	100.0	97.9	NP_756176	(chuW) Putative oxygen independent coproporphyrinogen III oxidase [Chu (VF0227)] [Escherichia coli CFT073]
contig00207	6985	7608	+	chuY	100.0	96.3	NP_756178	(chuY) ChuY [Chu (VF0227)] [Escherichia coli CFT073]
contig00168	3391	6435	+	cnf1	100.0	99.9	CAA50007	(cnf1) cytotoxic necrotizing factor 1 [CNF-1 (VF0240)] [Escherichia coli str. E-B35]
contig01217	1864	2319	+	csgB	99.8	83.8	NP_460114	(csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig01217	460	1110	-	csgD	100.0	81.1	NP_460113	(csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig01501	10	717	+	csgG	84.9	83.0	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00172	436	663	+	daaF	100.0	100.0	AAA23662	(daaF) DaaF protein [F1845 fimbrial adhesin (AI016)] [Escherichia coli str. C1845]
contig00659	1138	1581	-	draD	100.0	99.8	AAK16478	(draD) DraD periplasmic protein [Dr adhesins (VF0223)] [Escherichia coli O75:K5:H- str. IH11128]
contig00659	593	766	-	draP	100.0	99.4	AAK16479	(draP) DraP [Dr adhesins (VF0223)] [Escherichia coli O75:K5:H- str. IH11128]
contig01371	804	1550	+	entA	100.0	95.8	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig01371	1	804	+	entB	93.7	97.8	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00183	3542	4312	+	entD	100.0	94.0	NP_752599	(entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig02241	1	698	+	entD	90.5	93.3	NP_752599	(entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig01387	397	2007	+	entE	100.0	95.8	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00600	705	4534	-	entF	98.7	95.6	NP_752604	(entF) enterobactin synthase multienzyme complex component ATP-dependent [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig01377	1035	2072	-	entS	83.0	95.1	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig02345	2	1008	-	entS	80.5	95.7	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00208	3822	5720	-	espL1	100.0	95.0	NP_288154	(espL1) Type III secretion system effector espL1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00033	10632	11740	-	espR4	97.2	84.3	NP_288396	(espR4) Type III secretion system effector espR4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00897	580	2001	+	espX1	100.0	94.8	NP_285716	(espX1) Type III secretion system effector EspX1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00798	1614	3194	-	espX4	100.0	93.5	NP_290672	(espX4) Type III secretion system effector EspX4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00318	4757	6050	+	espX5	100.0	95.8	NP_290699	(espX5) Type III secretion system effector EspX5 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig01434	355	1103	+	espY1	99.5	94.4	NP_285753	(espY1) Type III secretion system effector EspY1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig01942	709	1278	-	espY2	100.0	94.0	NP_285765	(espY2) Type III secretion system effector EspY2 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig01030	1	2139	+	espY4	88.6	88.2	NP_290352	(espY4) Type III secretion system effector EspY4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00290	968	5193	+	fdeC	99.4	90.9	YP_002390132	(fdeC) adhesin FdeC [FdeC (VF0506)] [Escherichia coli O45:K1:H7 str. S88]
contig00183	1277	3517	+	fepA	100.0	96.8	NP_752600	(fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig01377	75	1031	+	fepB	100.0	97.3	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00871	1898	2713	+	fepC	100.0	97.2	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00871	1	912	+	fepD	89.7	95.9	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00871	909	1901	+	fepG	100.0	94.8	NP_752607	(fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00183	1	1034	-	fes	86.0	96.5	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00901	1004	1606	+	fimB	100.0	98.2	NP_757239	(fimB) Type 1 fimbriae Regulatory protein fimB [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00658	2529	3254	-	fimC	100.0	98.5	NP_757243	(fimC) Chaperone protein fimC precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00658	1	2462	-	fimD	93.4	98.2	NP_757244	(fimD) Outer membrane usher protein fimD precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00901	2084	2680	+	fimE	100.0	98.7	NP_757240	(fimE) Type 1 fimbriae Regulatory protein fimE [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig02603	186	719	-	fimF	100.0	97.4	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00640	1	803	+	fimH	88.0	97.5	NP_757248	(fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00658	3291	3830	-	fimI	100.0	98.3	NP_757242	(fimI) Fimbrin-like protein fimI precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00741	1016	1846	+	gspC	100.0	95.2	YP_404599	(gspC) general secretion pathway protein C [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00741	2086	3905	+	gspD	98.3	97.0	YP_404600	(gspD) general secretion pathway protein D [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00305	6065	7558	-	gspE	100.0	96.0	YP_404601	(gspE) general secretion pathway protein E [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00305	4866	6065	-	gspF	100.0	96.3	YP_404602	(gspF) general secretion pathway protein F [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig01633	474	1673	+	gspF	100.0	94.5	YP_404602	(gspF) general secretion pathway protein F [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00305	4370	4825	-	gspG	100.0	95.4	YP_404603	(gspG) general secretion pathway protein G [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00305	3803	4333	-	gspH	100.0	96.2	YP_404604	(gspH) general secretion pathway protein H [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig01766	608	1138	-	gspH	100.0	94.7	YP_404604	(gspH) general secretion pathway protein H [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00305	3435	3806	-	gspI	100.0	94.9	YP_404605	(gspI) general secretion pathway protein I [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig01766	240	611	-	gspI	100.0	92.2	YP_404605	(gspI) general secretion pathway protein I [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00305	2833	3402	-	gspJ	100.0	96.3	YP_404606	(gspJ) general secretion pathway protein J [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00305	1859	2836	-	gspK	100.0	97.7	YP_404607	(gspK) general secretion pathway protein K [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00305	684	1544	-	gspL	100.0	98.1	YP_404608	(gspL) general secretion pathway protein L [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig01787	120	980	+	gspL	100.0	95.1	YP_404608	(gspL) general secretion pathway protein L [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00305	146	568	-	gspM	100.0	97.4	YP_404609	(gspM) general secretion pathway protein M [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig01787	1096	1466	+	gspM	87.7	97.3	YP_404609	(gspM) general secretion pathway protein M [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00206	1	2993	-	hlyA	97.3	98.6	NP_755445	(hlyA) Hemolysin A [Hemolysin (VF0225)] [Escherichia coli CFT073]
contig00206	3005	3679	-	hlyC	100.0	100.0	NP_755444	(hlyC) Hemolysin C [Hemolysin (VF0225)] [Escherichia coli CFT073]
contig00168	1009	2445	+	hlyD	100.0	99.9	NP_755449	(hlyD) Hemolysin D [Hemolysin (VF0225)] [Escherichia coli CFT073]
contig00211	975	2762	+	iucA	100.0	94.3	NP_755502	(iucA) aerobactin siderophore biosynthesis protein IucD [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00211	2763	3710	+	iucB	100.0	95.7	NP_755501	(iucB) aerobactin siderophore biosynthesis protein IucB [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00211	3710	5452	+	iucC	100.0	96.1	NP_755500	(iucC) aerobactin siderophore biosynthesis protein IucC [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00211	5449	6770	+	iucD	98.8	96.3	NP_755499	(iucD) L-lysine 6-monooxygenase IucD [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00211	6708	9009	+	iutA	100.0	88.4	NP_755498	(iutA) ferric aerobactin receptor precusor IutA [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00229	2653	4329	+	kpsD	100.0	97.9	AAA21682	(kpsD) KpsD [K1 capsule (VF0239)] [Escherichia coli O18:K1:H7 str. RS218]
contig00278	3236	4288	-	ompA	100.0	94.0	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00132	3982	4296	-	papB	100.0	99.4		(papB) regulatory protein PapB [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig00132	1	2523	-	papC	100.0	99.7	NP_755465	(papC) usher protein PapC [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig00551	1609	2148	+	papE	100.0	100.0	NP_755460	(papE) P pilus minor subunit PapE [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig00551	2193	2723	+	papF	100.0	100.0	NP_755459	(papF) P pilus minor subunit PapF [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig00551	2767	3777	+	papG	100.0	99.1	NP_755458	(papG) P pilus tip adhesin PapG [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig00132	2570	3157	-	papH	100.0	98.0	NP_755466	(papH) P pilus termination subunit PapH [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig00132	4701	4934	+	papI	100.0	94.0	NP_755468	(papI) regulatory protein PapI [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig00551	473	1054	+	papJ	100.0	98.6	NP_755463	(papJ) P pilus assembly protein PapJ [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig00551	1061	1600	+	papK	100.0	99.3	NP_755461	(papK) P pilus minor subunit PapK [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig00551	4040	4591	+	papX	100.0	97.3	NP_755457	(papX) PapX protein regulates flagellum synthesis to repress motility [P fimbriae (CVF425)] [Escherichia coli CFT073]
contig00207	1541	3523	-	shuA	100.0	98.0	YP_405019	(shuA) outer membrane heme/hemoglobin receptor ShuA [Shu (VF0256)] [Shigella dysenteriae Sd197]
contig00207	6491	6985	+	shuX	100.0	96.6	YP_405016	(shuX) shu locus protein ShuX [Shu (VF0256)] [Shigella dysenteriae Sd197]
contig00107	12691	13403	-	yagV/ecpE	94.3	96.8	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig01628	1	713	+	yagV/ecpE	94.3	98.0	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00681	454	2979	+	yagX/ecpC	100.0	98.7	NP_286008	(yagX/ecpC) E. coli common pilus usher EcpC [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00883	2640	3227	+	yagZ/ecpA	100.0	99.3	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00736	2372	3331	-	ybtA	100.0	99.5	NP_405473	(ybtA) transcriptional regulator YbtA [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00948	156	959	-	ybtT	100.0	99.9	NP_405469	(ybtT) yersiniabactin biosynthetic protein YbtT [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00948	956	2056	-	ybtU	100.0	99.9	NP_405470	(ybtU) yersiniabactin biosynthetic protein YbtU [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00883	1975	2565	+	ykgK/ecpR	100.0	97.6	NP_286011	(ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

ID094LLFII

Contig	Start	End	Strand	Gene	Coverage	Identity	Accession	Product
contig00039	5109	5853	-	afaB-I	100.0	98.2	CAW30798	(afaB-I) chaperone AfaB [Afimbrial adhesin AFA-I mannose-resistant adhesin (AI010)] [Escherichia coli O25b:H4 str. FV9863]
contig00039	2434	5016	-	afaC-I	100.0	99.0	CAW30799	(afaC-I) usher AfaC [Afimbrial adhesin AFA-I mannose-resistant adhesin (AI010)] [Escherichia coli O25b:H4 str. FV9863]
contig00517	402	1830	+	aslA	100.0	97.1	AAG10151	(aslA) putative arylsulfatase [AslA (VF0238)] [Escherichia coli O18:K1:H7 str. RS218]
contig00022	8814	9842	-	chuS	100.0	96.4	NP_756169	(chuS) heme oxygenase ChuS [Chu (VF0227)] [Escherichia coli CFT073]
contig00022	16005	16997	+	chuU	100.0	96.6	NP_756179	(chuU) heme permease protein ChuU [Chu (VF0227)] [Escherichia coli CFT073]
contig00022	16964	17764	+	chuV	100.0	98.2	NP_756180	(chuV) ATP-binding hydrophilic protein ChuV [Chu (VF0227)] [Escherichia coli CFT073]
contig00022	13489	14826	+	chuW	100.0	96.8	NP_756176	(chuW) Putative oxygen independent coproporphyrinogen III oxidase [Chu (VF0227)] [Escherichia coli CFT073]
contig00022	15333	15956	+	chuY	100.0	96.5	NP_756178	(chuY) ChuY [Chu (VF0227)] [Escherichia coli CFT073]
contig01202	1	413	-	csgB	90.3	83.3	NP_460114	(csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00902	920	1336	+	csgF	99.0	81.0	NP_460111	(csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00039	7222	7449	+	daaF	100.0	100.0	AAA23662	(daaF) DaaF protein [F1845 fimbrial adhesin (AI016)] [Escherichia coli str. C1845]
contig00039	6114	6419	-	draA	100.0	100.0	AAK16475	(draA) cytoplamic protein DraA [Dr adhesins (VF0223)] [Escherichia coli O75:K5:H- str. IH11128]
contig00039	1975	2418	-	draD	100.0	99.8	AAK16478	(draD) DraD periplasmic protein [Dr adhesins (VF0223)] [Escherichia coli O75:K5:H- str. IH11128]
contig00039	677	1236	-	draE2	99.6	99.6	AAB65153	(draE2) Dr-II structural adhesin precursor [Afa/Dr family (VF0212)] [Escherichia coli EC7372]
contig00039	1423	1596	-	draP	100.0	99.4	AAK16479	(draP) DraP [Dr adhesins (VF0223)] [Escherichia coli O75:K5:H- str. IH11128]
contig00807	675	1421	+	entA	100.0	97.3	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00222	543	1730	-	entC	100.0	97.3	NP_752611	(entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00329	2044	2814	-	entD	100.0	92.7	NP_752599	(entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig01258	324	1094	-	entD	100.0	95.2	NP_752599	(entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00142	1552	5405	+	entF	99.3	95.5	NP_752604	(entF) enterobactin synthase multienzyme complex component ATP-dependent [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00222	2867	4117	-	entS	100.0	95.7	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00201	1146	3332	+	espL4	100.0	97.4	NP_290644	(espL4) Type III secretion system effector EspL4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00030	7753	9005	+	espR1	99.4	94.3	NP_287686	(espR1) Type III secretion system effector espR1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00983	1	1012	-	espR1	80.3	94.0	NP_287686	(espR1) Type III secretion system effector espR1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00054	8558	9666	-	espR4	97.2	84.7	NP_288396	(espR4) Type III secretion system effector espR4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00252	405	1826	+	espX1	100.0	96.0	NP_285716	(espX1) Type III secretion system effector EspX1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00229	3940	5520	+	espX4	100.0	95.8	NP_290672	(espX4) Type III secretion system effector EspX4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00052	6090	7382	-	espX5	100.0	95.9	NP_290699	(espX5) Type III secretion system effector EspX5 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00490	1828	2576	+	espY1	99.5	95.8	NP_285753	(espY1) Type III secretion system effector EspY1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00009	15490	16059	+	espY2	100.0	94.6	NP_285765	(espY2) Type III secretion system effector EspY2 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00120	4625	6196	+	espY3	100.0	95.5	NP_286160	(espY3) Type III secretion system effector EspY3 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00110	5547	7955	+	espY4	100.0	96.4	NP_290352	(espY4) Type III secretion system effector EspY4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00038	7724	11974	+	fdeC	100.0	95.1	YP_002390132	(fdeC) adhesin FdeC [FdeC (VF0506)] [Escherichia coli O45:K1:H7 str. S88]
contig00222	1907	2863	+	fepB	100.0	97.7	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00142	6779	7594	-	fepC	100.0	96.9	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00222	4216	5232	+	fepD	100.0	96.0	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00142	132	1334	+	fes	100.0	96.6	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig01951	2	495	+	fimG	98.0	97.8	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00575	3	801	+	fliG	80.5	80.5	YP_001006742	(fliG) flagellar motor switch protein G [Flagella (VF0394)] [Yersinia enterocolitica subsp. enterocolitica 8081]
contig00003	31711	33732	+	fyuA	100.0	99.9	NP_405467	(fyuA) pesticin/yersiniabactin receptor protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00004	7311	8141	+	gspC	100.0	95.2	YP_404599	(gspC) general secretion pathway protein C [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00004	8381	10231	+	gspD	100.0	96.1	YP_404600	(gspD) general secretion pathway protein D [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00004	10231	11724	+	gspE	100.0	95.0	YP_404601	(gspE) general secretion pathway protein E [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00004	11724	12923	+	gspF	100.0	94.2	YP_404602	(gspF) general secretion pathway protein F [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00004	12964	13419	+	gspG	100.0	96.0	YP_404603	(gspG) general secretion pathway protein G [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00004	13456	13986	+	gspH	100.0	94.7	YP_404604	(gspH) general secretion pathway protein H [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00004	13983	14354	+	gspI	100.0	92.2	YP_404605	(gspI) general secretion pathway protein I [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00004	14387	14956	+	gspJ	100.0	94.4	YP_404606	(gspJ) general secretion pathway protein J [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00004	14953	15930	+	gspK	100.0	96.6	YP_404607	(gspK) general secretion pathway protein K [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00004	16245	17105	+	gspL	100.0	94.8	YP_404608	(gspL) general secretion pathway protein L [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00004	17221	17642	+	gspM	99.8	92.7	YP_404609	(gspM) general secretion pathway protein M [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00012	15965	17194	+	iroD	100.0	99.7	NP_753166	(iroD) esterase [Salmochelin (IA013)] [Escherichia coli CFT073]
contig00012	17279	18238	+	iroE	100.0	98.7	NP_753165	(iroE) esterase [Salmochelin (IA013)] [Escherichia coli CFT073]
contig00003	18611	28102	+	irp1	100.0	99.7	NP_405471	(irp1) yersiniabactin biosynthetic protein Irp1 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00003	12416	18523	+	irp2	100.0	99.5	NP_405472	(irp2) yersiniabactin biosynthetic protein Irp2 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00035	7001	8788	+	iucA	100.0	94.3	NP_755502	(iucA) aerobactin siderophore biosynthesis protein IucD [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00035	8789	9736	+	iucB	100.0	95.6	NP_755501	(iucB) aerobactin siderophore biosynthesis protein IucB [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00035	9736	11478	+	iucC	100.0	96.1	NP_755500	(iucC) aerobactin siderophore biosynthesis protein IucC [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00035	11475	12796	+	iucD	98.8	96.3	NP_755499	(iucD) L-lysine 6-monooxygenase IucD [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00035	12734	15035	+	iutA	100.0	88.4	NP_755498	(iutA) ferric aerobactin receptor precusor IutA [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00004	32363	34039	-	kpsD	100.0	98.3	AAA21682	(kpsD) KpsD [K1 capsule (VF0239)] [Escherichia coli O18:K1:H7 str. RS218]
contig00004	18701	19477	+	kpsM	100.0	94.8	AAA24046	(kpsM) KpsM [K1 capsule (VF0239)] [Escherichia coli O18:K1:H7 str. RS218]
contig00140	3426	4478	-	ompA	100.0	95.2	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00792	958	1509	+	papX	100.0	97.5	NP_755457	(papX) PapX protein regulates flagellum synthesis to repress motility [P fimbriae (CVF425)] [Escherichia coli CFT073]
contig00022	9891	11873	-	shuA	100.0	98.5	YP_405019	(shuA) outer membrane heme/hemoglobin receptor ShuA [Shu (VF0256)] [Shigella dysenteriae Sd197]
contig00022	12478	13469	+	shuT	99.9	98.0	YP_405017	(shuT) periplasmic binding protein ShuT [Shu (VF0256)] [Shigella dysenteriae Sd197]
contig00022	14839	15333	+	shuX	100.0	96.4	YP_405016	(shuX) shu locus protein ShuX [Shu (VF0256)] [Shigella dysenteriae Sd197]
contig00011	614	1367	+	yagV/ecpE	99.7	97.0	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00363	2662	3330	+	yagY/ecpB	100.0	98.5	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00363	2018	2605	+	yagZ/ecpA	100.0	99.0	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig02264	65	566	+	yagZ/ecpA	85.4	99.2	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00003	11265	12224	+	ybtA	100.0	99.4	NP_405473	(ybtA) transcriptional regulator YbtA [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00003	30003	31580	+	ybtE	100.0	99.9	NP_405468	(ybtE) yersiniabactin siderophore biosynthetic protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00003	9296	11098	-	ybtP	100.0	99.7	NP_405474	(ybtP) lipoprotein inner membrane ABC-transporter [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00003	7507	9309	-	ybtQ	100.0	99.8	NP_405475	(ybtQ) inner membrane ABC-transporter YbtQ [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00003	4902	6206	-	ybtS	100.0	99.8	NP_405477	(ybtS) salicylate synthase Irp9 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00003	29196	29999	+	ybtT	100.0	99.6	NP_405469	(ybtT) yersiniabactin biosynthetic protein YbtT [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00003	28099	29199	+	ybtU	100.0	99.6	NP_405470	(ybtU) yersiniabactin biosynthetic protein YbtU [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00003	6234	7514	-	ybtX	100.0	99.6	NP_405476	(ybtX) putative signal transducer [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00363	1353	1943	+	ykgK/ecpR	100.0	99.0	NP_286011	(ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

ID099

Contig	Start	End	Strand	Gene	Coverage	Identity	Accession	Product
contig00001	473529	473984	-	csgB	99.8	84.0	NP_460114	(csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00001	474738	475388	+	csgD	100.0	81.1	NP_460113	(csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00001	475807	476223	+	csgF	99.0	81.2	NP_460111	(csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00001	476250	477083	+	csgG	100.0	83.1	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00010	99528	100274	-	entA	100.0	96.0	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00010	100274	101131	-	entB	100.0	97.9	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00010	102765	103952	-	entC	100.0	97.4	NP_752611	(entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00010	118596	119366	+	entD	100.0	94.0	NP_752599	(entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00010	101145	102755	-	entE	100.0	95.8	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00010	110839	114668	-	entF	98.7	95.4	NP_752604	(entF) enterobactin synthase multienzyme complex component ATP-dependent [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00010	105275	106525	-	entS	100.0	95.6	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00007	74456	76324	-	espL1	98.4	95.3	NP_288154	(espL1) Type III secretion system effector espL1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00033	24866	25921	+	espR1	83.8	94.2	NP_287686	(espR1) Type III secretion system effector espR1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00009	142345	143765	+	espX1	99.9	94.7	NP_285716	(espX1) Type III secretion system effector EspX1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00018	55513	57093	-	espX4	99.9	93.1	NP_290672	(espX4) Type III secretion system effector EspX4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00018	24701	25993	+	espX5	100.0	95.7	NP_290699	(espX5) Type III secretion system effector EspX5 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00014	43044	47285	-	fdeC	99.8	92.4	YP_002390132	(fdeC) adhesin FdeC [FdeC (VF0506)] [Escherichia coli O45:K1:H7 str. S88]
contig00010	116331	118571	+	fepA	100.0	96.8	NP_752600	(fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00010	104315	105271	+	fepB	100.0	97.4	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00010	108626	109441	+	fepC	100.0	97.3	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00010	106624	107640	+	fepD	100.0	96.0	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00010	107637	108629	+	fepG	100.0	94.0	NP_752607	(fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00010	114886	116088	-	fes	100.0	96.8	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00016	97591	98196	-	fimA	100.0	92.2	NP_757241	(fimA) Type-1 fimbrial protein A chain precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00038	1112	1714	-	fimB	100.0	98.2	NP_757239	(fimB) Type 1 fimbriae Regulatory protein fimB [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00016	96225	96950	-	fimC	100.0	98.5	NP_757243	(fimC) Chaperone protein fimC precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00016	93522	96158	-	fimD	100.0	98.3	NP_757244	(fimD) Outer membrane usher protein fimD precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00038	38	634	-	fimE	100.0	98.7	NP_757240	(fimE) Type 1 fimbriae Regulatory protein fimE [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00016	92982	93515	-	fimF	100.0	97.4	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00016	92466	92969	-	fimG	100.0	98.0	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00016	91544	92455	-	fimH	100.0	97.3	NP_757248	(fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00016	96987	97526	-	fimI	100.0	98.3	NP_757242	(fimI) Fimbrin-like protein fimI precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00002	353256	354086	-	gspC	100.0	95.1	YP_404599	(gspC) general secretion pathway protein C [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00002	351166	353016	-	gspD	100.0	97.0	YP_404600	(gspD) general secretion pathway protein D [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00002	349673	351166	-	gspE	100.0	97.1	YP_404601	(gspE) general secretion pathway protein E [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00002	348474	349673	-	gspF	100.0	96.2	YP_404602	(gspF) general secretion pathway protein F [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00002	347978	348433	-	gspG	100.0	95.6	YP_404603	(gspG) general secretion pathway protein G [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00002	347411	347941	-	gspH	100.0	96.0	YP_404604	(gspH) general secretion pathway protein H [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00002	347043	347414	-	gspI	100.0	95.2	YP_404605	(gspI) general secretion pathway protein I [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00002	346441	347010	-	gspJ	100.0	97.2	YP_404606	(gspJ) general secretion pathway protein J [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00002	345467	346444	-	gspK	100.0	96.1	YP_404607	(gspK) general secretion pathway protein K [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00002	344292	345152	-	gspL	100.0	97.6	YP_404608	(gspL) general secretion pathway protein L [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00002	343754	344176	-	gspM	100.0	94.1	YP_404609	(gspM) general secretion pathway protein M [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	546899	547951	+	ompA	100.0	94.3	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00014	56391	57144	+	yagV/ecpE	99.7	96.8	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00014	54824	56467	+	yagW/ecpD	100.0	98.6	NP_286007	(yagW/ecpD) polymerized tip adhesin of ECP fibers [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00014	52309	54834	+	yagX/ecpC	100.0	98.7	NP_286008	(yagX/ecpC) E. coli common pilus usher EcpC [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00014	51615	52283	+	yagY/ecpB	100.0	98.7	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00014	50970	51557	+	yagZ/ecpA	100.0	99.3	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00014	50305	50895	+	ykgK/ecpR	100.0	97.6	NP_286011	(ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

ID09CT

Contig	Start	End	Strand	Gene	Coverage	Identity	Accession	Product
contig00003	8284	8739	+	csgB	99.8	83.8	NP_460114	(csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00003	6880	7530	-	csgD	100.0	81.1	NP_460113	(csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00003	6045	6461	-	csgF	99.0	81.2	NP_460111	(csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00003	5185	6018	-	csgG	100.0	83.1	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00012	99363	100109	-	entA	100.0	96.0	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00012	100109	100966	-	entB	100.0	98.0	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00012	102600	103787	-	entC	100.0	97.6	NP_752611	(entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00012	118432	119202	+	entD	100.0	93.9	NP_752599	(entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00012	100980	102590	-	entE	100.0	96.2	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00012	110675	114504	-	entF	98.7	95.9	NP_752604	(entF) enterobactin synthase multienzyme complex component ATP-dependent [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00012	105110	106360	-	entS	100.0	95.6	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00002	245773	247671	-	espL1	100.0	94.9	NP_288154	(espL1) Type III secretion system effector espL1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00017	11613	12668	-	espR1	83.8	94.1	NP_287686	(espR1) Type III secretion system effector espR1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00033	18843	20263	+	espX1	99.9	94.3	NP_285716	(espX1) Type III secretion system effector EspX1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00020	55534	57115	-	espX4	99.9	92.9	NP_290672	(espX4) Type III secretion system effector EspX4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00020	24716	26008	+	espX5	100.0	95.5	NP_290699	(espX5) Type III secretion system effector EspX5 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00009	131886	136111	-	fdeC	99.4	91.8	YP_002390132	(fdeC) adhesin FdeC [FdeC (VF0506)] [Escherichia coli O45:K1:H7 str. S88]
contig00012	116167	118407	+	fepA	100.0	96.8	NP_752600	(fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00012	104150	105106	+	fepB	100.0	97.4	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00012	108461	109276	+	fepC	100.0	97.2	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00012	106459	107475	+	fepD	100.0	96.3	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00012	107472	108464	+	fepG	100.0	94.8	NP_752607	(fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00012	114722	115924	-	fes	100.0	96.5	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00019	100460	101064	-	fimA	99.8	90.6	NP_757241	(fimA) Type-1 fimbrial protein A chain precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00028	1110	1712	-	fimB	100.0	98.0	NP_757239	(fimB) Type 1 fimbriae Regulatory protein fimB [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00019	99094	99819	-	fimC	100.0	98.3	NP_757243	(fimC) Chaperone protein fimC precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00019	96391	99027	-	fimD	100.0	98.8	NP_757244	(fimD) Outer membrane usher protein fimD precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00028	36	632	-	fimE	100.0	98.5	NP_757240	(fimE) Type 1 fimbriae Regulatory protein fimE [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00019	95851	96384	-	fimF	100.0	97.0	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00019	95335	95838	-	fimG	100.0	97.8	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00019	94413	95324	-	fimH	100.0	97.3	NP_757248	(fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00019	99856	100395	-	fimI	100.0	98.7	NP_757242	(fimI) Fimbrin-like protein fimI precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00008	33909	34739	+	gspC	100.0	95.1	YP_404599	(gspC) general secretion pathway protein C [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00008	34979	36829	+	gspD	100.0	97.2	YP_404600	(gspD) general secretion pathway protein D [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00008	36829	38322	+	gspE	100.0	96.8	YP_404601	(gspE) general secretion pathway protein E [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00008	38322	39521	+	gspF	100.0	96.2	YP_404602	(gspF) general secretion pathway protein F [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00008	39562	40017	+	gspG	100.0	95.6	YP_404603	(gspG) general secretion pathway protein G [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00008	40054	40584	+	gspH	100.0	95.9	YP_404604	(gspH) general secretion pathway protein H [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00008	40581	40952	+	gspI	100.0	94.6	YP_404605	(gspI) general secretion pathway protein I [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00008	40985	41554	+	gspJ	100.0	97.2	YP_404606	(gspJ) general secretion pathway protein J [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00008	41551	42528	+	gspK	100.0	97.8	YP_404607	(gspK) general secretion pathway protein K [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00008	42843	43703	+	gspL	100.0	97.6	YP_404608	(gspL) general secretion pathway protein L [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00008	43819	44241	+	gspM	100.0	94.1	YP_404609	(gspM) general secretion pathway protein M [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00004	161723	162775	-	ompA	100.0	94.2	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00009	145195	145948	+	yagV/ecpE	99.7	96.8	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00009	143628	145271	+	yagW/ecpD	100.0	98.7	NP_286007	(yagW/ecpD) polymerized tip adhesin of ECP fibers [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00009	141113	143638	+	yagX/ecpC	100.0	98.7	NP_286008	(yagX/ecpC) E. coli common pilus usher EcpC [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00009	140419	141087	+	yagY/ecpB	100.0	98.2	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00009	139775	140362	+	yagZ/ecpA	100.0	99.3	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00009	139110	139700	+	ykgK/ecpR	100.0	97.6	NP_286011	(ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

ID101

Contig	Start	End	Strand	Gene	Coverage	Identity	Accession	Product
contig00001	289804	290259	-	csgB	99.8	84.0	NP_460114	(csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00001	291013	291663	+	csgD	100.0	81.1	NP_460113	(csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00001	292082	292498	+	csgF	99.0	81.2	NP_460111	(csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00001	292525	293358	+	csgG	100.0	83.1	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00008	100347	101093	-	entA	100.0	96.0	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00008	101093	101950	-	entB	100.0	97.9	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00008	103584	104771	-	entC	100.0	97.5	NP_752611	(entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00008	119415	120185	+	entD	100.0	94.0	NP_752599	(entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00008	101964	103574	-	entE	100.0	95.8	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00008	111658	115487	-	entF	98.7	95.4	NP_752604	(entF) enterobactin synthase multienzyme complex component ATP-dependent [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00008	106094	107344	-	entS	100.0	95.6	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00010	74456	76324	-	espL1	98.4	95.3	NP_288154	(espL1) Type III secretion system effector espL1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00031	24866	25921	+	espR1	83.8	94.2	NP_287686	(espR1) Type III secretion system effector espR1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00006	200547	201967	+	espX1	99.9	94.7	NP_285716	(espX1) Type III secretion system effector EspX1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00012	39590	41170	+	espX4	99.9	93.1	NP_290672	(espX4) Type III secretion system effector EspX4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00012	70690	71982	-	espX5	100.0	95.7	NP_290699	(espX5) Type III secretion system effector EspX5 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00017	43044	47285	-	fdeC	99.8	92.4	YP_002390132	(fdeC) adhesin FdeC [FdeC (VF0506)] [Escherichia coli O45:K1:H7 str. S88]
contig00008	117150	119390	+	fepA	100.0	96.8	NP_752600	(fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00008	105134	106090	+	fepB	100.0	97.4	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00008	109445	110260	+	fepC	100.0	97.3	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00008	107443	108459	+	fepD	100.0	96.0	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00008	108456	109448	+	fepG	100.0	94.0	NP_752607	(fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00008	115705	116907	-	fes	100.0	96.8	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00018	97591	98196	-	fimA	100.0	92.2	NP_757241	(fimA) Type-1 fimbrial protein A chain precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00036	26609	27211	+	fimB	100.0	98.2	NP_757239	(fimB) Type 1 fimbriae Regulatory protein fimB [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00018	96225	96950	-	fimC	100.0	98.5	NP_757243	(fimC) Chaperone protein fimC precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00018	93522	96158	-	fimD	100.0	98.3	NP_757244	(fimD) Outer membrane usher protein fimD precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00036	27689	28285	+	fimE	100.0	98.7	NP_757240	(fimE) Type 1 fimbriae Regulatory protein fimE [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00018	92982	93515	-	fimF	100.0	97.4	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00018	92466	92969	-	fimG	100.0	98.0	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00018	91544	92455	-	fimH	100.0	97.3	NP_757248	(fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00018	96987	97526	-	fimI	100.0	98.3	NP_757242	(fimI) Fimbrin-like protein fimI precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00002	353256	354086	-	gspC	100.0	95.1	YP_404599	(gspC) general secretion pathway protein C [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00002	351166	353016	-	gspD	100.0	97.0	YP_404600	(gspD) general secretion pathway protein D [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00002	349673	351166	-	gspE	100.0	97.1	YP_404601	(gspE) general secretion pathway protein E [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00002	348474	349673	-	gspF	100.0	96.2	YP_404602	(gspF) general secretion pathway protein F [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00002	347978	348433	-	gspG	100.0	95.6	YP_404603	(gspG) general secretion pathway protein G [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00002	347411	347941	-	gspH	100.0	96.0	YP_404604	(gspH) general secretion pathway protein H [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00002	347043	347414	-	gspI	100.0	95.2	YP_404605	(gspI) general secretion pathway protein I [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00002	346441	347010	-	gspJ	100.0	97.2	YP_404606	(gspJ) general secretion pathway protein J [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00002	345467	346444	-	gspK	100.0	96.1	YP_404607	(gspK) general secretion pathway protein K [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00002	344292	345152	-	gspL	100.0	97.6	YP_404608	(gspL) general secretion pathway protein L [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00002	343754	344176	-	gspM	100.0	94.1	YP_404609	(gspM) general secretion pathway protein M [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	363174	364226	+	ompA	100.0	94.3	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00017	56391	57144	+	yagV/ecpE	99.7	96.8	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00017	54824	56467	+	yagW/ecpD	100.0	98.6	NP_286007	(yagW/ecpD) polymerized tip adhesin of ECP fibers [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00017	52309	54834	+	yagX/ecpC	100.0	98.7	NP_286008	(yagX/ecpC) E. coli common pilus usher EcpC [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00017	51615	52283	+	yagY/ecpB	100.0	98.7	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00017	50970	51557	+	yagZ/ecpA	100.0	99.3	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00017	50305	50895	+	ykgK/ecpR	100.0	97.6	NP_286011	(ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

ID107II

Contig	Start	End	Strand	Gene	Coverage	Identity	Accession	Product
contig00018	66069	66374	-	afaA	100.0	99.7	CAW30797	(afaA) fimbrial major subunit AfaA [Afimbrial adhesin AFA-I mannose-resistant adhesin (AI010)] [Escherichia coli O25b:H4 str. FV9863]
contig00018	65055	65799	-	afaB-I	100.0	99.9	CAW30798	(afaB-I) chaperone AfaB [Afimbrial adhesin AFA-I mannose-resistant adhesin (AI010)] [Escherichia coli O25b:H4 str. FV9863]
contig00018	62380	64962	-	afaC-I	100.0	99.2	CAW30799	(afaC-I) usher AfaC [Afimbrial adhesin AFA-I mannose-resistant adhesin (AI010)] [Escherichia coli O25b:H4 str. FV9863]
contig00018	60692	61174	-	afaE-V	100.0	97.5	CAA62863	(afaE-V) AfaE-V adhesin [Afimbrial adhesin AFA-V (AI013)] [Escherichia coli str. AL 851]
contig00016	67310	68738	+	aslA	100.0	97.4	AAG10151	(aslA) putative arylsulfatase [AslA (VF0238)] [Escherichia coli O18:K1:H7 str. RS218]
contig00007	176915	177943	-	chuS	100.0	98.0	NP_756169	(chuS) heme oxygenase ChuS [Chu (VF0227)] [Escherichia coli CFT073]
contig00007	180580	181572	+	chuT	100.0	99.4	NP_756175	(chuT) periplasmic heme-binding protein ChuT [Chu (VF0227)] [Escherichia coli CFT073]
contig00007	184108	185100	+	chuU	100.0	99.1	NP_756179	(chuU) heme permease protein ChuU [Chu (VF0227)] [Escherichia coli CFT073]
contig00007	185067	185867	+	chuV	100.0	98.4	NP_756180	(chuV) ATP-binding hydrophilic protein ChuV [Chu (VF0227)] [Escherichia coli CFT073]
contig00007	181592	182929	+	chuW	100.0	97.9	NP_756176	(chuW) Putative oxygen independent coproporphyrinogen III oxidase [Chu (VF0227)] [Escherichia coli CFT073]
contig00007	183436	184059	+	chuY	100.0	96.3	NP_756178	(chuY) ChuY [Chu (VF0227)] [Escherichia coli CFT073]
contig00029	33947	36991	-	cnf1	100.0	99.9	CAA50007	(cnf1) cytotoxic necrotizing factor 1 [CNF-1 (VF0240)] [Escherichia coli str. E-B35]
contig00004	176502	176957	+	csgB	99.8	83.8	NP_460114	(csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00004	175096	175746	-	csgD	100.0	81.3	NP_460113	(csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00004	174261	174677	-	csgF	99.0	81.2	NP_460111	(csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00004	173401	174234	-	csgG	100.0	83.0	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00018	69707	69934	+	daaF	100.0	100.0	AAA23662	(daaF) DaaF protein [F1845 fimbrial adhesin (AI016)] [Escherichia coli str. C1845]
contig00018	61921	62364	-	draD	100.0	99.8	AAK16478	(draD) DraD periplasmic protein [Dr adhesins (VF0223)] [Escherichia coli O75:K5:H- str. IH11128]
contig00018	61376	61549	-	draP	100.0	99.4	AAK16479	(draP) DraP [Dr adhesins (VF0223)] [Escherichia coli O75:K5:H- str. IH11128]
contig00001	337365	338111	-	entA	100.0	96.4	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00001	338111	338968	-	entB	100.0	98.1	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00001	340602	341789	-	entC	100.0	98.4	NP_752611	(entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00001	356246	357016	+	entD	100.0	93.9	NP_752599	(entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00001	338982	340592	-	entE	100.0	96.5	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00001	348465	352318	-	entF	99.3	96.3	NP_752604	(entF) enterobactin synthase multienzyme complex component ATP-dependent [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00001	342926	344176	-	entS	100.0	96.3	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00005	161464	163362	-	espL1	100.0	96.0	NP_288154	(espL1) Type III secretion system effector espL1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00024	40325	41575	+	espR1	99.3	94.7	NP_287686	(espR1) Type III secretion system effector espR1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00003	202921	204342	+	espX1	100.0	93.2	NP_285716	(espX1) Type III secretion system effector EspX1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00017	57193	58773	+	espX4	100.0	96.0	NP_290672	(espX4) Type III secretion system effector EspX4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00003	163453	164201	-	espY1	99.5	94.4	NP_285753	(espY1) Type III secretion system effector EspY1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00003	146422	146991	-	espY2	100.0	94.0	NP_285765	(espY2) Type III secretion system effector EspY2 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00015	44734	47142	+	espY4	99.8	89.4	NP_290352	(espY4) Type III secretion system effector EspY4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00006	249146	253387	-	fdeC	99.8	92.0	YP_002390132	(fdeC) adhesin FdeC [FdeC (VF0506)] [Escherichia coli O45:K1:H7 str. S88]
contig00001	353981	356221	+	fepA	100.0	97.9	NP_752600	(fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00001	341966	342922	+	fepB	100.0	98.2	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00001	346277	347092	+	fepC	100.0	97.7	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00001	344275	345291	+	fepD	100.0	96.5	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00001	345288	346280	+	fepG	100.0	94.5	NP_752607	(fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00001	352536	353738	-	fes	100.0	97.0	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00003	345174	345779	-	fimA	100.0	92.6	NP_757241	(fimA) Type-1 fimbrial protein A chain precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00058	1111	1713	-	fimB	100.0	98.2	NP_757239	(fimB) Type 1 fimbriae Regulatory protein fimB [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00003	343808	344533	-	fimC	100.0	98.5	NP_757243	(fimC) Chaperone protein fimC precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00003	341105	343741	-	fimD	100.0	98.3	NP_757244	(fimD) Outer membrane usher protein fimD precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00058	37	633	-	fimE	100.0	98.7	NP_757240	(fimE) Type 1 fimbriae Regulatory protein fimE [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00003	340565	341098	-	fimF	100.0	97.4	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00003	340049	340552	-	fimG	100.0	97.8	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00003	339127	340038	-	fimH	100.0	97.3	NP_757248	(fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00003	344570	345109	-	fimI	100.0	98.3	NP_757242	(fimI) Fimbrin-like protein fimI precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00027	29363	31384	+	fyuA	100.0	99.8	NP_405467	(fyuA) pesticin/yersiniabactin receptor protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00030	33848	34678	+	gspC	100.0	94.7	YP_404599	(gspC) general secretion pathway protein C [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00030	34918	36768	+	gspD	100.0	96.1	YP_404600	(gspD) general secretion pathway protein D [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00030	36768	38261	+	gspE	100.0	94.6	YP_404601	(gspE) general secretion pathway protein E [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00030	38261	39460	+	gspF	100.0	94.5	YP_404602	(gspF) general secretion pathway protein F [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00030	39501	39956	+	gspG	100.0	96.3	YP_404603	(gspG) general secretion pathway protein G [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00030	39993	40523	+	gspH	100.0	94.7	YP_404604	(gspH) general secretion pathway protein H [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00030	40520	40891	+	gspI	100.0	92.2	YP_404605	(gspI) general secretion pathway protein I [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00030	40924	41493	+	gspJ	100.0	94.6	YP_404606	(gspJ) general secretion pathway protein J [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00030	41490	42467	+	gspK	100.0	96.5	YP_404607	(gspK) general secretion pathway protein K [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00030	42782	43642	+	gspL	100.0	95.0	YP_404608	(gspL) general secretion pathway protein L [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00030	43758	44179	+	gspM	99.8	97.4	YP_404609	(gspM) general secretion pathway protein M [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00029	41586	44660	-	hlyA	100.0	98.6	NP_755445	(hlyA) Hemolysin A [Hemolysin (VF0225)] [Escherichia coli CFT073]
contig00029	39392	41515	-	hlyB	100.0	99.2	NP_755448	(hlyB) Hemolysin B [Hemolysin (VF0225)] [Escherichia coli CFT073]
contig00029	44672	45346	-	hlyC	100.0	100.0	NP_755444	(hlyC) Hemolysin C [Hemolysin (VF0225)] [Escherichia coli CFT073]
contig00029	37937	39373	-	hlyD	100.0	99.9	NP_755449	(hlyD) Hemolysin D [Hemolysin (VF0225)] [Escherichia coli CFT073]
contig00027	16263	25754	+	irp1	100.0	99.7	NP_405471	(irp1) yersiniabactin biosynthetic protein Irp1 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00027	10068	16175	+	irp2	100.0	99.7	NP_405472	(irp2) yersiniabactin biosynthetic protein Irp2 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00053	7018	8805	+	iucA	100.0	94.3	NP_755502	(iucA) aerobactin siderophore biosynthesis protein IucD [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00053	8806	9753	+	iucB	100.0	95.7	NP_755501	(iucB) aerobactin siderophore biosynthesis protein IucB [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00053	9753	11495	+	iucC	100.0	96.1	NP_755500	(iucC) aerobactin siderophore biosynthesis protein IucC [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00053	11492	12813	+	iucD	98.8	96.3	NP_755499	(iucD) L-lysine 6-monooxygenase IucD [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00053	12751	15052	+	iutA	100.0	88.4	NP_755498	(iutA) ferric aerobactin receptor precusor IutA [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00047	12726	14402	-	kpsD	100.0	97.9	AAA21682	(kpsD) KpsD [K1 capsule (VF0239)] [Escherichia coli O18:K1:H7 str. RS218]
contig00030	45237	46013	+	kpsM	100.0	95.1	AAA24046	(kpsM) KpsM [K1 capsule (VF0239)] [Escherichia coli O18:K1:H7 str. RS218]
contig00004	104336	105376	-	ompA	100.0	98.1	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00029	13830	14144	-	papB	100.0	99.4		(papB) regulatory protein PapB [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig00029	9849	12371	-	papC	100.0	99.7	NP_755465	(papC) usher protein PapC [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig00029	9044	9649	-	papD	100.0	99.8	NP_755464	(papD) chaperone protein PapD [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig00029	7332	7871	-	papE	100.0	100.0	NP_755460	(papE) P pilus minor subunit PapE [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig00029	6757	7287	-	papF	100.0	100.0	NP_755459	(papF) P pilus minor subunit PapF [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig00029	5703	6713	-	papG	100.0	99.1	NP_755458	(papG) P pilus tip adhesin PapG [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig00029	12418	13005	-	papH	100.0	98.0	NP_755466	(papH) P pilus termination subunit PapH [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig00029	14549	14782	+	papI	100.0	94.0	NP_755468	(papI) regulatory protein PapI [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig00029	8426	9007	-	papJ	100.0	98.6	NP_755463	(papJ) P pilus assembly protein PapJ [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig00029	7880	8419	-	papK	100.0	99.3	NP_755461	(papK) P pilus minor subunit PapK [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig00029	4889	5440	-	papX	100.0	97.5	NP_755457	(papX) PapX protein regulates flagellum synthesis to repress motility [P fimbriae (CVF425)] [Escherichia coli CFT073]
contig00125	173	724	+	papX	100.0	97.5	NP_755457	(papX) PapX protein regulates flagellum synthesis to repress motility [P fimbriae (CVF425)] [Escherichia coli CFT073]
contig00007	177992	179974	-	shuA	100.0	98.0	YP_405019	(shuA) outer membrane heme/hemoglobin receptor ShuA [Shu (VF0256)] [Shigella dysenteriae Sd197]
contig00007	182942	183436	+	shuX	100.0	96.6	YP_405016	(shuX) shu locus protein ShuX [Shu (VF0256)] [Shigella dysenteriae Sd197]
contig00006	268799	269552	+	yagV/ecpE	99.7	98.1	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00006	267232	268875	+	yagW/ecpD	100.0	99.1	NP_286007	(yagW/ecpD) polymerized tip adhesin of ECP fibers [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00006	264717	267242	+	yagX/ecpC	100.0	98.5	NP_286008	(yagX/ecpC) E. coli common pilus usher EcpC [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00006	264023	264691	+	yagY/ecpB	100.0	99.0	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00006	263378	263965	+	yagZ/ecpA	100.0	99.0	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00027	8918	9877	+	ybtA	100.0	99.5	NP_405473	(ybtA) transcriptional regulator YbtA [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00027	27655	29232	+	ybtE	100.0	99.8	NP_405468	(ybtE) yersiniabactin siderophore biosynthetic protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00027	6949	8751	-	ybtP	100.0	99.6	NP_405474	(ybtP) lipoprotein inner membrane ABC-transporter [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00027	5160	6962	-	ybtQ	100.0	99.7	NP_405475	(ybtQ) inner membrane ABC-transporter YbtQ [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00027	2555	3859	-	ybtS	100.0	99.7	NP_405477	(ybtS) salicylate synthase Irp9 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00027	26848	27651	+	ybtT	100.0	99.9	NP_405469	(ybtT) yersiniabactin biosynthetic protein YbtT [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00027	25751	26851	+	ybtU	100.0	99.9	NP_405470	(ybtU) yersiniabactin biosynthetic protein YbtU [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00027	3887	5167	-	ybtX	100.0	99.5	NP_405476	(ybtX) putative signal transducer [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00006	262713	263303	+	ykgK/ecpR	100.0	99.7	NP_286011	(ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

ID124

Contig	Start	End	Strand	Gene	Coverage	Identity	Accession	Product
contig00018	49279	50707	+	aslA	100.0	93.6	AAG10151	(aslA) putative arylsulfatase [AslA (VF0238)] [Escherichia coli O18:K1:H7 str. RS218]
contig00016	8267	8722	+	csgB	99.8	83.8	NP_460114	(csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00016	6862	7512	-	csgD	100.0	81.1	NP_460113	(csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00016	6027	6443	-	csgF	99.0	81.2	NP_460111	(csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00016	5167	6000	-	csgG	100.0	83.5	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00011	99075	99821	-	entA	100.0	95.7	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00011	99821	100678	-	entB	100.0	98.1	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00011	102312	103499	-	entC	100.0	97.9	NP_752611	(entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00011	118143	118913	+	entD	100.0	95.2	NP_752599	(entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00011	100692	102302	-	entE	100.0	95.5	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00011	110362	114215	-	entF	99.3	95.7	NP_752604	(entF) enterobactin synthase multienzyme complex component ATP-dependent [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00011	104822	106072	-	entS	100.0	95.4	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00001	66391	68290	-	espL1	100.0	97.6	NP_288154	(espL1) Type III secretion system effector espL1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00033	37584	39770	+	espL4	100.0	97.3	NP_290644	(espL4) Type III secretion system effector EspL4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00039	25267	26320	+	espR1	83.7	93.8	NP_287686	(espR1) Type III secretion system effector espR1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00003	203260	204681	+	espX1	100.0	93.2	NP_285716	(espX1) Type III secretion system effector EspX1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00033	7788	9368	-	espX4	99.9	93.2	NP_290672	(espX4) Type III secretion system effector EspX4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00053	94	1386	+	espX5	100.0	97.1	NP_290699	(espX5) Type III secretion system effector EspX5 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00003	164302	165113	-	espY1	99.9	87.0	NP_285753	(espY1) Type III secretion system effector EspY1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00020	73944	78192	-	fdeC	99.9	94.2	YP_002390132	(fdeC) adhesin FdeC [FdeC (VF0506)] [Escherichia coli O45:K1:H7 str. S88]
contig00011	115878	118118	+	fepA	100.0	96.7	NP_752600	(fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00011	103862	104818	+	fepB	100.0	97.5	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00011	108173	108988	+	fepC	100.0	97.3	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00011	106171	107187	+	fepD	100.0	96.1	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00011	107184	108176	+	fepG	100.0	94.1	NP_752607	(fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00011	114433	115635	-	fes	100.0	96.7	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00043	25238	25849	-	fimA	100.0	88.6	NP_757241	(fimA) Type-1 fimbrial protein A chain precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00043	27347	27949	-	fimB	100.0	98.2	NP_757239	(fimB) Type 1 fimbriae Regulatory protein fimB [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00043	23872	24597	-	fimC	100.0	98.9	NP_757243	(fimC) Chaperone protein fimC precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00043	21169	23805	-	fimD	100.0	98.6	NP_757244	(fimD) Outer membrane usher protein fimD precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00043	26276	26870	-	fimE	99.7	99.3	NP_757240	(fimE) Type 1 fimbriae Regulatory protein fimE [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00043	20629	21162	-	fimF	100.0	97.9	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00043	20113	20616	-	fimG	100.0	97.8	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00043	19191	20102	-	fimH	100.0	97.4	NP_757248	(fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00043	24634	25173	-	fimI	100.0	98.7	NP_757242	(fimI) Fimbrin-like protein fimI precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00006	52965	53795	-	gspC	100.0	94.7	YP_404599	(gspC) general secretion pathway protein C [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00006	50875	52725	-	gspD	100.0	96.1	YP_404600	(gspD) general secretion pathway protein D [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00006	49382	50875	-	gspE	100.0	96.9	YP_404601	(gspE) general secretion pathway protein E [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00006	48183	49382	-	gspF	100.0	96.0	YP_404602	(gspF) general secretion pathway protein F [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00006	47687	48142	-	gspG	100.0	95.0	YP_404603	(gspG) general secretion pathway protein G [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00006	47121	47650	-	gspH	99.8	94.9	YP_404604	(gspH) general secretion pathway protein H [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00006	46753	47124	-	gspI	100.0	95.2	YP_404605	(gspI) general secretion pathway protein I [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00006	46151	46720	-	gspJ	100.0	96.7	YP_404606	(gspJ) general secretion pathway protein J [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00006	45177	46154	-	gspK	100.0	97.0	YP_404607	(gspK) general secretion pathway protein K [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00006	44002	44862	-	gspL	100.0	97.0	YP_404608	(gspL) general secretion pathway protein L [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00006	43464	43886	-	gspM	100.0	98.3	YP_404609	(gspM) general secretion pathway protein M [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00005	145353	146393	-	ompA	100.0	98.1	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00073	2274	2586	-	papB	99.4	99.0		(papB) regulatory protein PapB [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig00073	3009	3229	+	papI	94.4	98.6	NP_755468	(papI) regulatory protein PapI [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig00055	5439	6192	+	yagV/ecpE	99.7	97.1	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00055	3872	5515	+	yagW/ecpD	100.0	99.1	NP_286007	(yagW/ecpD) polymerized tip adhesin of ECP fibers [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00055	1357	3882	+	yagX/ecpC	100.0	98.8	NP_286008	(yagX/ecpC) E. coli common pilus usher EcpC [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00055	663	1331	+	yagY/ecpB	100.0	98.1	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00055	18	605	+	yagZ/ecpA	100.0	99.2	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00020	81214	81804	+	ykgK/ecpR	100.0	97.0	NP_286011	(ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

ID127

Contig	Start	End	Strand	Gene	Coverage	Identity	Accession	Product
contig00020	49272	50700	+	aslA	100.0	93.6	AAG10151	(aslA) putative arylsulfatase [AslA (VF0238)] [Escherichia coli O18:K1:H7 str. RS218]
contig00018	8267	8722	+	csgB	99.8	83.8	NP_460114	(csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00018	6862	7512	-	csgD	100.0	81.1	NP_460113	(csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00018	6027	6443	-	csgF	99.0	81.2	NP_460111	(csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00018	5167	6000	-	csgG	100.0	83.5	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00016	99075	99821	-	entA	100.0	95.7	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00016	99821	100678	-	entB	100.0	98.1	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00016	102312	103499	-	entC	100.0	97.9	NP_752611	(entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00016	118143	118913	+	entD	100.0	95.2	NP_752599	(entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00016	100692	102302	-	entE	100.0	95.5	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00016	110362	114215	-	entF	99.3	95.7	NP_752604	(entF) enterobactin synthase multienzyme complex component ATP-dependent [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00016	104822	106072	-	entS	100.0	95.4	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00002	66391	68290	-	espL1	100.0	97.6	NP_288154	(espL1) Type III secretion system effector espL1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00031	37583	39769	+	espL4	100.0	97.3	NP_290644	(espL4) Type III secretion system effector EspL4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00035	25267	26320	+	espR1	83.7	93.8	NP_287686	(espR1) Type III secretion system effector espR1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00004	25291	26425	-	espR4	99.5	84.3	NP_288396	(espR4) Type III secretion system effector espR4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00001	50504	51925	-	espX1	100.0	93.2	NP_285716	(espX1) Type III secretion system effector EspX1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00031	7787	9367	-	espX4	99.9	93.2	NP_290672	(espX4) Type III secretion system effector EspX4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00030	31378	32670	+	espX5	100.0	97.1	NP_290699	(espX5) Type III secretion system effector EspX5 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00001	90075	90886	+	espY1	99.9	87.0	NP_285753	(espY1) Type III secretion system effector EspY1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00016	115878	118118	+	fepA	100.0	96.7	NP_752600	(fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00016	103862	104818	+	fepB	100.0	97.5	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00016	108173	108988	+	fepC	100.0	97.3	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00016	106171	107187	+	fepD	100.0	96.1	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00016	107184	108176	+	fepG	100.0	94.1	NP_752607	(fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00016	114433	115635	-	fes	100.0	96.7	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00038	25238	25849	-	fimA	100.0	88.6	NP_757241	(fimA) Type-1 fimbrial protein A chain precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00038	27347	27949	-	fimB	100.0	98.2	NP_757239	(fimB) Type 1 fimbriae Regulatory protein fimB [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00038	23872	24597	-	fimC	100.0	98.9	NP_757243	(fimC) Chaperone protein fimC precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00038	21169	23805	-	fimD	100.0	98.6	NP_757244	(fimD) Outer membrane usher protein fimD precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00038	26276	26870	-	fimE	99.7	99.3	NP_757240	(fimE) Type 1 fimbriae Regulatory protein fimE [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00038	20629	21162	-	fimF	100.0	97.9	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00038	20113	20616	-	fimG	100.0	97.8	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00038	19191	20102	-	fimH	100.0	97.4	NP_757248	(fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00038	24634	25173	-	fimI	100.0	98.7	NP_757242	(fimI) Fimbrin-like protein fimI precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00004	86337	88358	+	fyuA	100.0	99.9	NP_405467	(fyuA) pesticin/yersiniabactin receptor protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00009	30434	31264	+	gspC	100.0	94.7	YP_404599	(gspC) general secretion pathway protein C [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00009	31504	33354	+	gspD	100.0	96.1	YP_404600	(gspD) general secretion pathway protein D [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00009	33354	34847	+	gspE	100.0	96.9	YP_404601	(gspE) general secretion pathway protein E [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00009	34847	36046	+	gspF	100.0	96.0	YP_404602	(gspF) general secretion pathway protein F [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00009	36087	36542	+	gspG	100.0	95.0	YP_404603	(gspG) general secretion pathway protein G [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00009	36579	37108	+	gspH	99.8	94.9	YP_404604	(gspH) general secretion pathway protein H [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00009	37105	37476	+	gspI	100.0	94.9	YP_404605	(gspI) general secretion pathway protein I [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00009	37509	38078	+	gspJ	100.0	96.7	YP_404606	(gspJ) general secretion pathway protein J [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00009	38075	39052	+	gspK	100.0	97.0	YP_404607	(gspK) general secretion pathway protein K [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00009	39367	40227	+	gspL	100.0	97.0	YP_404608	(gspL) general secretion pathway protein L [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00009	40343	40765	+	gspM	100.0	98.3	YP_404609	(gspM) general secretion pathway protein M [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00004	73237	82728	+	irp1	100.0	99.3	NP_405471	(irp1) yersiniabactin biosynthetic protein Irp1 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00004	67042	73149	+	irp2	100.0	99.8	NP_405472	(irp2) yersiniabactin biosynthetic protein Irp2 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00005	145353	146393	-	ompA	100.0	98.1	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00004	65892	66851	+	ybtA	100.0	99.5	NP_405473	(ybtA) transcriptional regulator YbtA [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00004	84629	86206	+	ybtE	100.0	99.8	NP_405468	(ybtE) yersiniabactin siderophore biosynthetic protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00004	63923	65725	-	ybtP	100.0	99.6	NP_405474	(ybtP) lipoprotein inner membrane ABC-transporter [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00004	62134	63936	-	ybtQ	100.0	99.7	NP_405475	(ybtQ) inner membrane ABC-transporter YbtQ [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00004	59529	60833	-	ybtS	100.0	99.9	NP_405477	(ybtS) salicylate synthase Irp9 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00004	83822	84625	+	ybtT	100.0	99.8	NP_405469	(ybtT) yersiniabactin biosynthetic protein YbtT [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00004	82725	83825	+	ybtU	100.0	100.0	NP_405470	(ybtU) yersiniabactin biosynthetic protein YbtU [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00004	60861	62141	-	ybtX	100.0	99.7	NP_405476	(ybtX) putative signal transducer [Yersiniabactin (VF0136)] [Yersinia pestis CO92]

ID128

Contig	Start	End	Strand	Gene	Coverage	Identity	Accession	Product
contig00017	71089	72517	+	aslA	100.0	98.2	AAG10151	(aslA) putative arylsulfatase [AslA (VF0238)] [Escherichia coli O18:K1:H7 str. RS218]
contig00010	172126	174072	-	chuA	100.0	99.5	NP_756170	(chuA) Outer membrane heme/hemoglobin receptor ChuA [Chu (VF0227)] [Escherichia coli CFT073]
contig00010	171049	172077	-	chuS	100.0	99.0	NP_756169	(chuS) heme oxygenase ChuS [Chu (VF0227)] [Escherichia coli CFT073]
contig00010	174714	175706	+	chuT	100.0	99.8	NP_756175	(chuT) periplasmic heme-binding protein ChuT [Chu (VF0227)] [Escherichia coli CFT073]
contig00010	178242	179234	+	chuU	100.0	99.5	NP_756179	(chuU) heme permease protein ChuU [Chu (VF0227)] [Escherichia coli CFT073]
contig00010	179201	180001	+	chuV	100.0	99.8	NP_756180	(chuV) ATP-binding hydrophilic protein ChuV [Chu (VF0227)] [Escherichia coli CFT073]
contig00010	175726	177063	+	chuW	100.0	98.9	NP_756176	(chuW) Putative oxygen independent coproporphyrinogen III oxidase [Chu (VF0227)] [Escherichia coli CFT073]
contig00010	177076	177570	+	chuX	100.0	100.0	NP_756177	(chuX) putative heme-binding protein ChuX [Chu (VF0227)] [Escherichia coli CFT073]
contig00010	177570	178193	+	chuY	100.0	98.2	NP_756178	(chuY) ChuY [Chu (VF0227)] [Escherichia coli CFT073]
contig00006	103007	103462	-	csgB	99.8	83.8	NP_460114	(csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00006	104215	104865	+	csgD	100.0	81.6	NP_460113	(csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00006	105284	105700	+	csgF	99.0	80.8	NP_460111	(csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00006	105727	106560	+	csgG	100.0	83.2	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00002	281540	282286	-	entA	100.0	98.1	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00002	282286	283143	-	entB	100.0	99.4	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00002	284777	285964	-	entC	100.0	98.7	NP_752611	(entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00002	300453	301114	+	entD	85.9	96.7	NP_752599	(entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00002	283157	284767	-	entE	100.0	98.9	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00002	292644	296525	-	entF	100.0	98.2	NP_752604	(entF) enterobactin synthase multienzyme complex component ATP-dependent [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00002	287101	288351	-	entS	100.0	97.4	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00013	47884	52131	-	fdeC	99.9	97.4	YP_002390132	(fdeC) adhesin FdeC [FdeC (VF0506)] [Escherichia coli O45:K1:H7 str. S88]
contig00002	298188	300428	+	fepA	100.0	98.9	NP_752600	(fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00002	286141	287097	+	fepB	100.0	98.4	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00002	290452	291267	+	fepC	100.0	99.1	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00002	288450	289466	+	fepD	100.0	97.8	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00002	289463	290455	+	fepG	100.0	97.9	NP_752607	(fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00002	296743	297945	-	fes	100.0	98.9	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00004	331497	332101	-	fimA	99.8	90.8	NP_757241	(fimA) Type-1 fimbrial protein A chain precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00004	330131	330856	-	fimC	100.0	98.9	NP_757243	(fimC) Chaperone protein fimC precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00004	327428	330064	-	fimD	100.0	98.5	NP_757244	(fimD) Outer membrane usher protein fimD precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00004	332524	333120	-	fimE	100.0	98.8	NP_757240	(fimE) Type 1 fimbriae Regulatory protein fimE [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00004	326888	327421	-	fimF	100.0	96.6	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00004	326372	326875	-	fimG	100.0	98.2	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00004	325450	326361	-	fimH	100.0	97.5	NP_757248	(fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00004	330893	331432	-	fimI	100.0	98.5	NP_757242	(fimI) Fimbrin-like protein fimI precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00016	57323	59344	-	fyuA	100.0	99.8	NP_405467	(fyuA) pesticin/yersiniabactin receptor protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00003	47338	48168	-	gspC	100.0	93.9	YP_404599	(gspC) general secretion pathway protein C [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00003	45248	47098	-	gspD	100.0	96.1	YP_404600	(gspD) general secretion pathway protein D [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00003	43755	45248	-	gspE	100.0	95.0	YP_404601	(gspE) general secretion pathway protein E [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00003	42556	43755	-	gspF	100.0	94.2	YP_404602	(gspF) general secretion pathway protein F [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00003	42060	42515	-	gspG	100.0	96.3	YP_404603	(gspG) general secretion pathway protein G [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00003	41493	42023	-	gspH	100.0	94.7	YP_404604	(gspH) general secretion pathway protein H [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00003	41125	41496	-	gspI	100.0	92.2	YP_404605	(gspI) general secretion pathway protein I [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00003	40523	41092	-	gspJ	100.0	94.4	YP_404606	(gspJ) general secretion pathway protein J [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00003	39549	40526	-	gspK	100.0	96.5	YP_404607	(gspK) general secretion pathway protein K [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00003	38374	39234	-	gspL	100.0	94.1	YP_404608	(gspL) general secretion pathway protein L [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00003	37840	38258	-	gspM	99.0	93.1	YP_404609	(gspM) general secretion pathway protein M [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00016	62953	72444	-	irp1	100.0	99.8	NP_405471	(irp1) yersiniabactin biosynthetic protein Irp1 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00016	72532	78639	-	irp2	100.0	99.5	NP_405472	(irp2) yersiniabactin biosynthetic protein Irp2 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00028	8836	10617	+	iucA	100.0	99.8	NP_709454	(iucA) aerobactin synthesis protein IucA [Aerobactin (VF0123)] [Shigella flexneri 2a str. 301]
contig00028	10618	11565	+	iucB	100.0	99.8	NP_709455	(iucB) aerobactin synthesis protein IucB [Aerobactin (VF0123)] [Shigella flexneri 2a str. 301]
contig00028	11565	13307	+	iucC	100.0	98.2	NP_755500	(iucC) aerobactin siderophore biosynthesis protein IucC [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00028	13304	14625	+	iucD	98.8	96.3	NP_755499	(iucD) L-lysine 6-monooxygenase IucD [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00028	14563	16864	+	iutA	100.0	88.4	NP_755498	(iutA) ferric aerobactin receptor precusor IutA [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00003	24930	26606	+	kpsD	100.0	98.3	AAA21682	(kpsD) KpsD [K1 capsule (VF0239)] [Escherichia coli O18:K1:H7 str. RS218]
contig00003	35860	36636	-	kpsM	100.0	95.4	AAA24046	(kpsM) KpsM [K1 capsule (VF0239)] [Escherichia coli O18:K1:H7 str. RS218]
contig00006	173433	174485	+	ompA	100.0	95.8	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00028	750	1063	-	papB	99.7	98.4		(papB) regulatory protein PapB [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig00028	1468	1701	+	papI	100.0	94.9	NP_755468	(papI) regulatory protein PapI [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig00062	256	807	+	papX	100.0	97.6	NP_755457	(papX) PapX protein regulates flagellum synthesis to repress motility [P fimbriae (CVF425)] [Escherichia coli CFT073]
contig00028	17796	21695	+	sat	100.0	99.6	NP_755494	(sat) Aecreted auto transpoter toxin [Sat (VF0231)] [Escherichia coli CFT073]
contig00013	67469	68222	+	yagV/ecpE	99.7	98.0	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00013	65902	67545	+	yagW/ecpD	100.0	99.2	NP_286007	(yagW/ecpD) polymerized tip adhesin of ECP fibers [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00013	63387	65912	+	yagX/ecpC	100.0	97.6	NP_286008	(yagX/ecpC) E. coli common pilus usher EcpC [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00013	62693	63361	+	yagY/ecpB	100.0	98.1	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00013	62049	62636	+	yagZ/ecpA	100.0	98.5	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00016	78830	79789	-	ybtA	100.0	99.3	NP_405473	(ybtA) transcriptional regulator YbtA [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00016	59475	61052	-	ybtE	100.0	99.8	NP_405468	(ybtE) yersiniabactin siderophore biosynthetic protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00016	79956	81758	+	ybtP	100.0	99.6	NP_405474	(ybtP) lipoprotein inner membrane ABC-transporter [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00016	81745	83547	+	ybtQ	100.0	99.6	NP_405475	(ybtQ) inner membrane ABC-transporter YbtQ [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00016	84848	86152	+	ybtS	100.0	99.8	NP_405477	(ybtS) salicylate synthase Irp9 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00016	61056	61859	-	ybtT	100.0	99.6	NP_405469	(ybtT) yersiniabactin biosynthetic protein YbtT [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00016	61856	62956	-	ybtU	100.0	99.7	NP_405470	(ybtU) yersiniabactin biosynthetic protein YbtU [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00016	83540	84820	+	ybtX	100.0	99.7	NP_405476	(ybtX) putative signal transducer [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00013	61384	61974	+	ykgK/ecpR	100.0	99.5	NP_286011	(ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

ID129E

Contig	Start	End	Strand	Gene	Coverage	Identity	Accession	Product
contig00003	254364	254819	-	csgB	99.8	83.8	NP_460114	(csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00003	255573	256223	+	csgD	100.0	81.1	NP_460113	(csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00003	256642	257058	+	csgF	99.0	81.2	NP_460111	(csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00003	257085	257918	+	csgG	100.0	83.1	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00007	99273	100019	-	entA	100.0	95.8	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00007	100019	100876	-	entB	100.0	97.5	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00007	102510	103697	-	entC	100.0	97.6	NP_752611	(entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00007	118341	119111	+	entD	100.0	93.3	NP_752599	(entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00007	100890	102500	-	entE	100.0	95.7	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00007	110560	114413	-	entF	99.3	95.6	NP_752604	(entF) enterobactin synthase multienzyme complex component ATP-dependent [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00007	105020	106270	-	entS	100.0	95.5	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00012	65768	67666	-	espL1	100.0	94.8	NP_288154	(espL1) Type III secretion system effector espL1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00025	38965	40020	-	espR1	83.8	94.2	NP_287686	(espR1) Type III secretion system effector espR1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00032	18863	20284	+	espX1	100.0	94.4	NP_285716	(espX1) Type III secretion system effector EspX1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00016	45992	47572	+	espX4	99.9	93.0	NP_290672	(espX4) Type III secretion system effector EspX4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00016	116375	117667	-	espX5	100.0	95.5	NP_290699	(espX5) Type III secretion system effector EspX5 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00017	46877	51102	-	fdeC	99.4	92.8	YP_002390132	(fdeC) adhesin FdeC [FdeC (VF0506)] [Escherichia coli O45:K1:H7 str. S88]
contig00007	116076	118316	+	fepA	100.0	96.9	NP_752600	(fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00007	104060	105016	+	fepB	100.0	97.5	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00007	108371	109186	+	fepC	100.0	97.3	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00007	106369	107385	+	fepD	100.0	96.5	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00007	107382	108374	+	fepG	100.0	94.0	NP_752607	(fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00007	114631	115833	-	fes	100.0	96.5	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00022	100499	101104	-	fimA	100.0	91.1	NP_757241	(fimA) Type-1 fimbrial protein A chain precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00015	1121	1723	-	fimB	100.0	97.8	NP_757239	(fimB) Type 1 fimbriae Regulatory protein fimB [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00022	99133	99858	-	fimC	100.0	98.3	NP_757243	(fimC) Chaperone protein fimC precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00022	96430	99066	-	fimD	100.0	98.8	NP_757244	(fimD) Outer membrane usher protein fimD precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00015	47	643	-	fimE	100.0	99.2	NP_757240	(fimE) Type 1 fimbriae Regulatory protein fimE [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00022	95890	96423	-	fimF	100.0	96.4	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00022	95374	95877	-	fimG	100.0	97.6	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00022	94452	95363	-	fimH	100.0	97.8	NP_757248	(fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00022	99895	100434	-	fimI	100.0	98.0	NP_757242	(fimI) Fimbrin-like protein fimI precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00002	372113	372943	-	gspC	100.0	95.0	YP_404599	(gspC) general secretion pathway protein C [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00002	370023	371873	-	gspD	100.0	97.1	YP_404600	(gspD) general secretion pathway protein D [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00002	368530	370023	-	gspE	100.0	96.0	YP_404601	(gspE) general secretion pathway protein E [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00002	367331	368530	-	gspF	100.0	96.8	YP_404602	(gspF) general secretion pathway protein F [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00002	366835	367290	-	gspG	100.0	96.3	YP_404603	(gspG) general secretion pathway protein G [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00002	366268	366798	-	gspH	100.0	95.3	YP_404604	(gspH) general secretion pathway protein H [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00002	365900	366271	-	gspI	100.0	95.2	YP_404605	(gspI) general secretion pathway protein I [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00002	365298	365867	-	gspJ	100.0	97.2	YP_404606	(gspJ) general secretion pathway protein J [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00002	364324	365301	-	gspK	100.0	97.7	YP_404607	(gspK) general secretion pathway protein K [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00002	363149	364009	-	gspL	100.0	97.6	YP_404608	(gspL) general secretion pathway protein L [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00002	362611	363033	-	gspM	100.0	93.8	YP_404609	(gspM) general secretion pathway protein M [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00013	123759	124811	+	ompA	100.0	94.7	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00017	60209	60962	+	yagV/ecpE	99.7	96.8	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00017	58642	60285	+	yagW/ecpD	100.0	98.6	NP_286007	(yagW/ecpD) polymerized tip adhesin of ECP fibers [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00017	56127	58652	+	yagX/ecpC	100.0	98.7	NP_286008	(yagX/ecpC) E. coli common pilus usher EcpC [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00017	55433	56101	+	yagY/ecpB	100.0	98.5	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00017	54788	55375	+	yagZ/ecpA	100.0	99.3	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00017	54123	54713	+	ykgK/ecpR	100.0	97.8	NP_286011	(ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

ID130

Contig	Start	End	Strand	Gene	Coverage	Identity	Accession	Product
contig00014	57551	58958	+	aslA	98.5	92.2	AAG10151	(aslA) putative arylsulfatase [AslA (VF0238)] [Escherichia coli O18:K1:H7 str. RS218]
contig00003	377573	378028	+	csgB	99.8	83.6	NP_460114	(csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00003	376168	376818	-	csgD	100.0	81.3	NP_460113	(csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00003	375333	375749	-	csgF	99.0	81.2	NP_460111	(csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00003	374473	375306	-	csgG	100.0	83.2	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00012	99238	99984	-	entA	100.0	95.7	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00012	99984	100841	-	entB	100.0	98.1	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00012	102475	103662	-	entC	100.0	97.9	NP_752611	(entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00012	118306	119076	+	entD	100.0	94.3	NP_752599	(entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00012	100855	102465	-	entE	100.0	95.5	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00012	110525	114378	-	entF	99.3	95.7	NP_752604	(entF) enterobactin synthase multienzyme complex component ATP-dependent [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00012	104985	106235	-	entS	100.0	95.4	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00001	505701	507599	-	espL1	100.0	97.5	NP_288154	(espL1) Type III secretion system effector espL1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00019	73495	75681	+	espL4	100.0	97.3	NP_290644	(espL4) Type III secretion system effector EspL4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00024	25251	26305	+	espR1	83.7	93.9	NP_287686	(espR1) Type III secretion system effector espR1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00006	202150	203570	+	espX1	99.9	95.0	NP_285716	(espX1) Type III secretion system effector EspX1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00019	43685	45265	-	espX4	99.9	93.2	NP_290672	(espX4) Type III secretion system effector EspX4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00019	12895	14187	+	espX5	100.0	96.5	NP_290699	(espX5) Type III secretion system effector EspX5 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00016	33673	37921	-	fdeC	99.9	94.3	YP_002390132	(fdeC) adhesin FdeC [FdeC (VF0506)] [Escherichia coli O45:K1:H7 str. S88]
contig00012	116041	118281	+	fepA	100.0	96.8	NP_752600	(fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00012	104025	104981	+	fepB	100.0	97.4	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00012	108336	109151	+	fepC	100.0	97.3	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00012	106334	107350	+	fepD	100.0	96.1	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00012	107347	108339	+	fepG	100.0	94.1	NP_752607	(fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00012	114596	115798	-	fes	100.0	96.7	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00015	94960	95571	-	fimA	100.0	88.4	NP_757241	(fimA) Type-1 fimbrial protein A chain precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00031	18766	19368	+	fimB	100.0	97.7	NP_757239	(fimB) Type 1 fimbriae Regulatory protein fimB [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00015	93594	94319	-	fimC	100.0	98.3	NP_757243	(fimC) Chaperone protein fimC precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00015	90891	93527	-	fimD	100.0	98.4	NP_757244	(fimD) Outer membrane usher protein fimD precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00031	19845	20439	+	fimE	99.7	99.2	NP_757240	(fimE) Type 1 fimbriae Regulatory protein fimE [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00015	90351	90884	-	fimF	100.0	97.6	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00015	89835	90338	-	fimG	100.0	98.0	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00015	88913	89824	-	fimH	100.0	97.3	NP_757248	(fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00015	94356	94895	-	fimI	100.0	98.7	NP_757242	(fimI) Fimbrin-like protein fimI precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00001	244222	246243	-	fyuA	100.0	99.7	NP_405467	(fyuA) pesticin/yersiniabactin receptor protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00001	249852	259343	-	irp1	100.0	99.7	NP_405471	(irp1) yersiniabactin biosynthetic protein Irp1 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00001	259431	265538	-	irp2	100.0	99.7	NP_405472	(irp2) yersiniabactin biosynthetic protein Irp2 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00003	303382	304422	-	ompA	100.0	98.1	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00016	47027	47780	+	yagV/ecpE	99.7	97.0	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00016	45460	47103	+	yagW/ecpD	100.0	99.1	NP_286007	(yagW/ecpD) polymerized tip adhesin of ECP fibers [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00016	42945	45470	+	yagX/ecpC	100.0	98.7	NP_286008	(yagX/ecpC) E. coli common pilus usher EcpC [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00016	42251	42919	+	yagY/ecpB	100.0	98.1	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00016	41606	42193	+	yagZ/ecpA	100.0	99.0	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00001	265729	266688	-	ybtA	100.0	99.2	NP_405473	(ybtA) transcriptional regulator YbtA [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00001	246374	247951	-	ybtE	100.0	99.8	NP_405468	(ybtE) yersiniabactin siderophore biosynthetic protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00001	266855	268657	+	ybtP	100.0	99.5	NP_405474	(ybtP) lipoprotein inner membrane ABC-transporter [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00001	268644	270446	+	ybtQ	100.0	99.6	NP_405475	(ybtQ) inner membrane ABC-transporter YbtQ [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00001	271747	273051	+	ybtS	100.0	99.8	NP_405477	(ybtS) salicylate synthase Irp9 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00001	247955	248758	-	ybtT	100.0	99.6	NP_405469	(ybtT) yersiniabactin biosynthetic protein YbtT [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00001	248755	249855	-	ybtU	100.0	99.1	NP_405470	(ybtU) yersiniabactin biosynthetic protein YbtU [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00001	270439	271719	+	ybtX	100.0	99.5	NP_405476	(ybtX) putative signal transducer [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00016	40941	41531	+	ykgK/ecpR	100.0	96.8	NP_286011	(ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

ID134

Contig	Start	End	Strand	Gene	Coverage	Identity	Accession	Product
contig00324	1	1174	+	aslA	82.1	92.7	AAG10151	(aslA) putative arylsulfatase [AslA (VF0238)] [Escherichia coli O18:K1:H7 str. RS218]
contig00856	303	719	+	csgF	99.0	81.2	NP_460111	(csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00856	746	1579	+	csgG	100.0	83.5	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig01945	110	943	+	csgG	100.0	83.0	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig01852	431	1068	-	entA	85.4	96.2	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00082	2387	3157	+	entD	100.0	93.3	NP_752599	(entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00228	105	875	-	entD	100.0	95.2	NP_752599	(entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00543	1	1515	+	entE	94.0	95.1	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig01014	1	1515	+	entE	94.0	95.5	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00338	234	2133	+	espL1	100.0	97.6	NP_288154	(espL1) Type III secretion system effector espL1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00659	76	1974	-	espL1	100.0	94.7	NP_288154	(espL1) Type III secretion system effector espL1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig01226	1	1417	+	espX4	89.6	96.3	NP_290672	(espX4) Type III secretion system effector EspX4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig01239	1	1405	+	espX4	88.8	93.4	NP_290672	(espX4) Type III secretion system effector EspX4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00161	2245	3537	+	espX5	100.0	95.5	NP_290699	(espX5) Type III secretion system effector EspX5 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00660	637	1418	+	espY1	99.9	90.4	NP_285753	(espY1) Type III secretion system effector EspY1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00061	1058	5283	-	fdeC	99.4	92.8	YP_002390132	(fdeC) adhesin FdeC [FdeC (VF0506)] [Escherichia coli O45:K1:H7 str. S88]
contig00082	122	2362	+	fepA	100.0	96.9	NP_752600	(fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00228	900	3140	-	fepA	100.0	96.7	NP_752600	(fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00909	506	1522	+	fepD	100.0	95.9	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00155	1	1052	+	fes	87.5	96.4	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00263	1	1052	+	fes	87.5	96.3	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00836	802	1407	-	fimA	100.0	90.1	NP_757241	(fimA) Type-1 fimbrial protein A chain precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig01274	715	1320	-	fimA	100.0	91.1	NP_757241	(fimA) Type-1 fimbrial protein A chain precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00758	1203	1736	-	fimF	100.0	96.4	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00758	687	1190	-	fimG	100.0	97.6	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00836	199	737	-	fimI	99.8	98.7	NP_757242	(fimI) Fimbrin-like protein fimI precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig01274	111	650	-	fimI	100.0	98.0	NP_757242	(fimI) Fimbrin-like protein fimI precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00110	2360	3190	+	gspC	100.0	96.6	YP_404599	(gspC) general secretion pathway protein C [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00249	751	1581	+	gspC	100.0	95.0	YP_404599	(gspC) general secretion pathway protein C [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig01259	1	993	+	gspF	82.8	95.6	YP_404602	(gspF) general secretion pathway protein F [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig01262	1	993	+	gspF	82.8	96.4	YP_404602	(gspF) general secretion pathway protein F [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00004	54086	54508	-	gspM	100.0	93.8	YP_404609	(gspM) general secretion pathway protein M [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig02024	340	762	-	gspM	100.0	98.3	YP_404609	(gspM) general secretion pathway protein M [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig02423	1	854	+	ompA	82.0	97.8	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00031	3816	4569	+	yagV/ecpE	99.7	96.8	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00031	2249	3892	+	yagW/ecpD	100.0	98.6	NP_286007	(yagW/ecpD) polymerized tip adhesin of ECP fibers [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00031	1	2259	+	yagX/ecpC	89.4	98.5	NP_286008	(yagX/ecpC) E. coli common pilus usher EcpC [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig01362	400	1068	+	yagY/ecpB	100.0	98.5	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

ID136

Contig	Start	End	Strand	Gene	Coverage	Identity	Accession	Product
contig00015	107924	108379	-	csgB	99.8	84.0	NP_460114	(csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00015	109133	109783	+	csgD	100.0	81.1	NP_460113	(csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00015	110202	110618	+	csgF	99.0	81.2	NP_460111	(csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00015	110645	111478	+	csgG	100.0	83.1	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00007	99457	100203	-	entA	100.0	96.0	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00007	100203	101060	-	entB	100.0	97.9	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00007	102694	103881	-	entC	100.0	97.5	NP_752611	(entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00007	118525	119295	+	entD	100.0	94.0	NP_752599	(entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00007	101074	102684	-	entE	100.0	95.8	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00007	110768	114597	-	entF	98.7	95.4	NP_752604	(entF) enterobactin synthase multienzyme complex component ATP-dependent [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00007	105204	106454	-	entS	100.0	95.6	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00009	74456	76324	-	espL1	98.4	95.3	NP_288154	(espL1) Type III secretion system effector espL1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00032	24866	25921	+	espR1	83.8	94.2	NP_287686	(espR1) Type III secretion system effector espR1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00013	142351	143771	+	espX1	99.9	94.7	NP_285716	(espX1) Type III secretion system effector EspX1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00017	55522	57102	-	espX4	99.9	93.1	NP_290672	(espX4) Type III secretion system effector EspX4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00017	24711	26003	+	espX5	100.0	95.7	NP_290699	(espX5) Type III secretion system effector EspX5 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00022	43044	47285	-	fdeC	99.8	92.4	YP_002390132	(fdeC) adhesin FdeC [FdeC (VF0506)] [Escherichia coli O45:K1:H7 str. S88]
contig00007	116260	118500	+	fepA	100.0	96.8	NP_752600	(fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00007	104244	105200	+	fepB	100.0	97.4	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00007	108555	109370	+	fepC	100.0	97.3	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00007	106553	107569	+	fepD	100.0	96.0	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00007	107566	108558	+	fepG	100.0	94.0	NP_752607	(fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00007	114815	116017	-	fes	100.0	96.8	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00016	107592	108196	-	fimA	99.8	90.6	NP_757241	(fimA) Type-1 fimbrial protein A chain precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00035	39364	39966	+	fimB	100.0	97.8	NP_757239	(fimB) Type 1 fimbriae Regulatory protein fimB [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00016	106220	106945	-	fimC	100.0	98.6	NP_757243	(fimC) Chaperone protein fimC precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00016	103517	106153	-	fimD	100.0	98.7	NP_757244	(fimD) Outer membrane usher protein fimD precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00035	40444	41040	+	fimE	100.0	99.2	NP_757240	(fimE) Type 1 fimbriae Regulatory protein fimE [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00016	102977	103510	-	fimF	100.0	96.6	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00016	102461	102964	-	fimG	100.0	97.8	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00016	101539	102450	-	fimH	100.0	97.7	NP_757248	(fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00016	106988	107527	-	fimI	100.0	99.1	NP_757242	(fimI) Fimbrin-like protein fimI precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00001	379409	380239	-	gspC	100.0	95.1	YP_404599	(gspC) general secretion pathway protein C [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	377319	379169	-	gspD	100.0	97.0	YP_404600	(gspD) general secretion pathway protein D [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	375826	377319	-	gspE	100.0	97.1	YP_404601	(gspE) general secretion pathway protein E [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	374627	375826	-	gspF	100.0	96.2	YP_404602	(gspF) general secretion pathway protein F [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	374131	374586	-	gspG	100.0	95.6	YP_404603	(gspG) general secretion pathway protein G [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	373564	374094	-	gspH	100.0	96.0	YP_404604	(gspH) general secretion pathway protein H [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	373196	373567	-	gspI	100.0	95.2	YP_404605	(gspI) general secretion pathway protein I [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	372594	373163	-	gspJ	100.0	97.2	YP_404606	(gspJ) general secretion pathway protein J [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	371620	372597	-	gspK	100.0	96.1	YP_404607	(gspK) general secretion pathway protein K [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	370445	371305	-	gspL	100.0	97.6	YP_404608	(gspL) general secretion pathway protein L [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	369907	370329	-	gspM	100.0	94.1	YP_404609	(gspM) general secretion pathway protein M [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00011	98754	99806	-	ompA	100.0	94.3	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00022	56391	57144	+	yagV/ecpE	99.7	96.8	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00022	54824	56467	+	yagW/ecpD	100.0	98.5	NP_286007	(yagW/ecpD) polymerized tip adhesin of ECP fibers [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00022	52309	54834	+	yagX/ecpC	100.0	98.7	NP_286008	(yagX/ecpC) E. coli common pilus usher EcpC [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00022	51615	52283	+	yagY/ecpB	100.0	98.7	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00022	50970	51557	+	yagZ/ecpA	100.0	99.3	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00022	50305	50895	+	ykgK/ecpR	100.0	97.6	NP_286011	(ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

ID141

Contig	Start	End	Strand	Gene	Coverage	Identity	Accession	Product
contig00203	1	641	+	entA	85.8	98.3	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00416	1	532	-	fimA	87.8	89.7	NP_757241	(fimA) Type-1 fimbrial protein A chain precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00177	147	460	-	papB	99.7	98.4		(papB) regulatory protein PapB [P fimbriae (VF0220)] [Escherichia coli CFT073]

ID142

Contig	Start	End	Strand	Gene	Coverage	Identity	Accession	Product
contig01476	48	801	-	yagV/ecpE	99.7	85.3	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00024	1825	3307	+	yagW/ecpD	90.2	88.0	NP_286007	(yagW/ecpD) polymerized tip adhesin of ECP fibers [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

ID164

Contig	Start	End	Strand	Gene	Coverage	Identity	Accession	Product
contig00038	14769	16197	+	aslA	100.0	93.6	AAG10151	(aslA) putative arylsulfatase [AslA (VF0238)] [Escherichia coli O18:K1:H7 str. RS218]
contig00102	1987	2103	-	astA	100.0	99.1	BAA94855	(astA) heat-stable enterotoxin 1 [EAST1 (VF0216)] [Escherichia coli O44:H18 042]
contig00034	8267	8722	+	csgB	99.8	83.8	NP_460114	(csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00034	6862	7512	-	csgD	100.0	81.1	NP_460113	(csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00034	6027	6443	-	csgF	99.0	81.2	NP_460111	(csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00034	5167	6000	-	csgG	100.0	83.5	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00013	99134	99880	-	entA	100.0	95.7	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00013	99880	100737	-	entB	100.0	98.0	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00013	102371	103558	-	entC	100.0	97.9	NP_752611	(entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00013	118202	118972	+	entD	100.0	95.2	NP_752599	(entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00013	100751	102361	-	entE	100.0	95.5	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00013	110421	114274	-	entF	99.3	95.7	NP_752604	(entF) enterobactin synthase multienzyme complex component ATP-dependent [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00013	104881	106131	-	entS	100.0	95.4	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00004	19954	21853	-	espL1	100.0	97.5	NP_288154	(espL1) Type III secretion system effector espL1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00050	19362	21548	+	espL4	100.0	97.3	NP_290644	(espL4) Type III secretion system effector EspL4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00040	25904	26957	+	espR1	83.7	93.8	NP_287686	(espR1) Type III secretion system effector espR1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00016	87218	88639	+	espX1	100.0	95.2	NP_285716	(espX1) Type III secretion system effector EspX1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00007	164243	165823	-	espX4	99.9	93.3	NP_290672	(espX4) Type III secretion system effector EspX4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00007	133452	134744	+	espX5	100.0	97.1	NP_290699	(espX5) Type III secretion system effector EspX5 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00016	48263	49074	-	espY1	99.9	87.0	NP_285753	(espY1) Type III secretion system effector EspY1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00056	15640	16140	-	faeC	91.8	87.1	AAL47165	(faeC) FaeC [K88 pili/F4 fimbriae (AI040)] [Escherichia coli]
contig00056	13180	15518	-	faeD	95.9	94.1	YP_002295985	(faeD) fimbrial usher protein FaeD [K88 pili/F4 fimbriae (AI040)] [Escherichia coli SE11]
contig00056	12465	13187	-	faeE	93.0	94.3	YP_002295986	(faeE) fimbrial chaperone FaeE [K88 pili/F4 fimbriae (AI040)] [Escherichia coli SE11]
contig00056	11870	12361	-	faeF	100.0	93.5	YP_002295987	(faeF) fimbrial protein FaeF [K88 pili/F4 fimbriae (AI040)] [Escherichia coli SE11]
contig00056	9830	10627	-	faeH	100.0	84.8	YP_002295989	(faeH) fimbrial protein FaeH [K88 pili/F4 fimbriae (AI040)] [Escherichia coli SE11]
contig00056	9035	9798	-	faeI	99.9	89.1	YP_002295990	(faeI) fimbrial protein FaeI [K88 pili/F4 fimbriae (AI040)] [Escherichia coli SE11]
contig00056	8245	9018	-	faeJ	100.0	94.2	YP_002295991	(faeJ) fimbrial protein FaeJ [K88 pili/F4 fimbriae (AI040)] [Escherichia coli SE11]
contig00026	33580	37828	-	fdeC	99.9	94.2	YP_002390132	(fdeC) adhesin FdeC [FdeC (VF0506)] [Escherichia coli O45:K1:H7 str. S88]
contig00013	115937	118177	+	fepA	100.0	96.7	NP_752600	(fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00013	103921	104877	+	fepB	100.0	97.5	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00013	108232	109047	+	fepC	100.0	97.3	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00013	106230	107246	+	fepD	100.0	96.1	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00013	107243	108235	+	fepG	100.0	94.1	NP_752607	(fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00013	114492	115694	-	fes	100.0	96.7	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00024	31397	33418	-	fyuA	100.0	99.9	NP_405467	(fyuA) pesticin/yersiniabactin receptor protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00024	37027	46518	-	irp1	100.0	99.8	NP_405471	(irp1) yersiniabactin biosynthetic protein Irp1 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00024	46606	52713	-	irp2	100.0	99.8	NP_405472	(irp2) yersiniabactin biosynthetic protein Irp2 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00060	7017	8804	+	iucA	100.0	94.2	NP_755502	(iucA) aerobactin siderophore biosynthesis protein IucD [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00060	8805	9752	+	iucB	100.0	95.6	NP_755501	(iucB) aerobactin siderophore biosynthesis protein IucB [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00060	9752	11494	+	iucC	100.0	96.0	NP_755500	(iucC) aerobactin siderophore biosynthesis protein IucC [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00060	11491	12812	+	iucD	98.8	96.3	NP_755499	(iucD) L-lysine 6-monooxygenase IucD [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00060	12750	15051	+	iutA	100.0	88.4	NP_755498	(iutA) ferric aerobactin receptor precusor IutA [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00017	20305	21345	-	ompA	100.0	98.1	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00026	46935	47688	+	yagV/ecpE	99.7	97.1	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00026	45368	47011	+	yagW/ecpD	100.0	99.1	NP_286007	(yagW/ecpD) polymerized tip adhesin of ECP fibers [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00026	42853	45378	+	yagX/ecpC	100.0	98.8	NP_286008	(yagX/ecpC) E. coli common pilus usher EcpC [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00026	42159	42827	+	yagY/ecpB	100.0	98.1	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00026	41514	42101	+	yagZ/ecpA	100.0	99.2	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00024	52904	53863	-	ybtA	100.0	99.9	NP_405473	(ybtA) transcriptional regulator YbtA [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00024	33549	35126	-	ybtE	100.0	99.9	NP_405468	(ybtE) yersiniabactin siderophore biosynthetic protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00024	54030	55832	+	ybtP	100.0	99.8	NP_405474	(ybtP) lipoprotein inner membrane ABC-transporter [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00024	55819	57621	+	ybtQ	100.0	99.9	NP_405475	(ybtQ) inner membrane ABC-transporter YbtQ [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00024	58922	60226	+	ybtS	100.0	99.9	NP_405477	(ybtS) salicylate synthase Irp9 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00024	35130	35933	-	ybtT	100.0	99.2	NP_405469	(ybtT) yersiniabactin biosynthetic protein YbtT [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00024	35930	37030	-	ybtU	100.0	100.0	NP_405470	(ybtU) yersiniabactin biosynthetic protein YbtU [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00024	57614	58894	+	ybtX	100.0	99.9	NP_405476	(ybtX) putative signal transducer [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00026	40849	41439	+	ykgK/ecpR	100.0	97.0	NP_286011	(ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

ID169

Contig	Start	End	Strand	Gene	Coverage	Identity	Accession	Product
contig00022	73365	73670	-	afaA	100.0	100.0	CAW30797	(afaA) fimbrial major subunit AfaA [Afimbrial adhesin AFA-I mannose-resistant adhesin (AI010)] [Escherichia coli O25b:H4 str. FV9863]
contig00022	72344	73088	-	afaB-I	100.0	99.6	CAW30798	(afaB-I) chaperone AfaB [Afimbrial adhesin AFA-I mannose-resistant adhesin (AI010)] [Escherichia coli O25b:H4 str. FV9863]
contig00022	69669	72251	-	afaC-I	100.0	99.9	CAW30799	(afaC-I) usher AfaC [Afimbrial adhesin AFA-I mannose-resistant adhesin (AI010)] [Escherichia coli O25b:H4 str. FV9863]
contig00022	69210	69653	-	afaD	100.0	100.0	CAW30800	(afaD) AfaD [Afimbrial adhesin AFA-I mannose-resistant adhesin (AI010)] [Escherichia coli O25b:H4 str. FV9863]
contig00022	67972	68457	-	afaE-I	100.0	99.8	CAW30801	(afaE-I) AFA-I adhesin [Afa/Dr family (VF0212)] [Escherichia coli O25b:H4 str. FV9863]
contig00018	71089	72517	+	aslA	100.0	98.2	AAG10151	(aslA) putative arylsulfatase [AslA (VF0238)] [Escherichia coli O18:K1:H7 str. RS218]
contig00006	172126	174072	-	chuA	100.0	99.5	NP_756170	(chuA) Outer membrane heme/hemoglobin receptor ChuA [Chu (VF0227)] [Escherichia coli CFT073]
contig00006	171049	172077	-	chuS	100.0	99.0	NP_756169	(chuS) heme oxygenase ChuS [Chu (VF0227)] [Escherichia coli CFT073]
contig00006	174714	175706	+	chuT	100.0	99.8	NP_756175	(chuT) periplasmic heme-binding protein ChuT [Chu (VF0227)] [Escherichia coli CFT073]
contig00006	178242	179234	+	chuU	100.0	99.5	NP_756179	(chuU) heme permease protein ChuU [Chu (VF0227)] [Escherichia coli CFT073]
contig00006	179201	180001	+	chuV	100.0	99.8	NP_756180	(chuV) ATP-binding hydrophilic protein ChuV [Chu (VF0227)] [Escherichia coli CFT073]
contig00006	175726	177063	+	chuW	100.0	98.9	NP_756176	(chuW) Putative oxygen independent coproporphyrinogen III oxidase [Chu (VF0227)] [Escherichia coli CFT073]
contig00006	177076	177570	+	chuX	100.0	100.0	NP_756177	(chuX) putative heme-binding protein ChuX [Chu (VF0227)] [Escherichia coli CFT073]
contig00006	177570	178193	+	chuY	100.0	98.2	NP_756178	(chuY) ChuY [Chu (VF0227)] [Escherichia coli CFT073]
contig00032	13547	14002	-	csgB	99.8	83.8	NP_460114	(csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00032	14755	15405	+	csgD	100.0	81.6	NP_460113	(csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00032	15824	16240	+	csgF	99.0	80.8	NP_460111	(csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00032	16267	17100	+	csgG	100.0	83.2	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00022	74588	74815	+	daaF	100.0	100.0	AAA23662	(daaF) DaaF protein [F1845 fimbrial adhesin (AI016)] [Escherichia coli str. C1845]
contig00022	68659	68832	-	draP	100.0	98.8	AAK16479	(draP) DraP [Dr adhesins (VF0223)] [Escherichia coli O75:K5:H- str. IH11128]
contig00001	281532	282278	-	entA	100.0	98.1	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00001	282278	283135	-	entB	100.0	99.4	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00001	284769	285956	-	entC	100.0	98.7	NP_752611	(entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00001	300445	301106	+	entD	85.9	96.7	NP_752599	(entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00001	283149	284759	-	entE	100.0	98.9	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00001	292636	296517	-	entF	100.0	98.2	NP_752604	(entF) enterobactin synthase multienzyme complex component ATP-dependent [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00001	287093	288343	-	entS	100.0	97.4	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00005	206173	210420	-	fdeC	99.9	97.4	YP_002390132	(fdeC) adhesin FdeC [FdeC (VF0506)] [Escherichia coli O45:K1:H7 str. S88]
contig00001	298180	300420	+	fepA	100.0	98.9	NP_752600	(fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00001	286133	287089	+	fepB	100.0	98.4	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00001	290444	291259	+	fepC	100.0	99.1	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00001	288442	289458	+	fepD	100.0	97.8	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00001	289455	290447	+	fepG	100.0	97.9	NP_752607	(fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00001	296735	297937	-	fes	100.0	99.0	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00027	63546	64150	-	fimA	99.8	90.8	NP_757241	(fimA) Type-1 fimbrial protein A chain precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00027	62180	62905	-	fimC	100.0	98.9	NP_757243	(fimC) Chaperone protein fimC precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00027	59477	62113	-	fimD	100.0	98.5	NP_757244	(fimD) Outer membrane usher protein fimD precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00070	8989	9585	+	fimE	100.0	98.8	NP_757240	(fimE) Type 1 fimbriae Regulatory protein fimE [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00027	58937	59470	-	fimF	100.0	96.6	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00027	58421	58924	-	fimG	100.0	98.2	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00027	57499	58410	-	fimH	100.0	97.5	NP_757248	(fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00027	62942	63481	-	fimI	100.0	98.5	NP_757242	(fimI) Fimbrin-like protein fimI precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00034	41502	43523	-	fyuA	100.0	99.8	NP_405467	(fyuA) pesticin/yersiniabactin receptor protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00008	5172	6002	-	gspC	100.0	93.9	YP_404599	(gspC) general secretion pathway protein C [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00008	3082	4932	-	gspD	100.0	96.1	YP_404600	(gspD) general secretion pathway protein D [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00008	1589	3082	-	gspE	100.0	95.0	YP_404601	(gspE) general secretion pathway protein E [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00008	390	1589	-	gspF	100.0	94.2	YP_404602	(gspF) general secretion pathway protein F [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00069	112	642	+	gspH	100.0	94.7	YP_404604	(gspH) general secretion pathway protein H [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00069	639	1010	+	gspI	100.0	92.2	YP_404605	(gspI) general secretion pathway protein I [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00069	1043	1612	+	gspJ	100.0	94.4	YP_404606	(gspJ) general secretion pathway protein J [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00069	1609	2586	+	gspK	100.0	96.6	YP_404607	(gspK) general secretion pathway protein K [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00069	2901	3761	+	gspL	100.0	94.8	YP_404608	(gspL) general secretion pathway protein L [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00069	3877	4298	+	gspM	99.8	92.9	YP_404609	(gspM) general secretion pathway protein M [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00050	11815	17922	+	irp2	100.0	99.4	NP_405472	(irp2) yersiniabactin biosynthetic protein Irp2 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00048	9495	11276	+	iucA	100.0	99.8	NP_709454	(iucA) aerobactin synthesis protein IucA [Aerobactin (VF0123)] [Shigella flexneri 2a str. 301]
contig00048	11277	12224	+	iucB	100.0	99.8	NP_709455	(iucB) aerobactin synthesis protein IucB [Aerobactin (VF0123)] [Shigella flexneri 2a str. 301]
contig00048	12224	13966	+	iucC	100.0	98.2	NP_755500	(iucC) aerobactin siderophore biosynthesis protein IucC [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00048	13963	15284	+	iucD	98.8	96.3	NP_755499	(iucD) L-lysine 6-monooxygenase IucD [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00048	15222	17523	+	iutA	100.0	88.4	NP_755498	(iutA) ferric aerobactin receptor precusor IutA [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00054	8799	10475	-	kpsD	100.0	98.3	AAA21682	(kpsD) KpsD [K1 capsule (VF0239)] [Escherichia coli O18:K1:H7 str. RS218]
contig00069	5357	6133	+	kpsM	100.0	94.7	AAA24046	(kpsM) KpsM [K1 capsule (VF0239)] [Escherichia coli O18:K1:H7 str. RS218]
contig00011	1054	2106	+	ompA	100.0	95.8	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00048	1409	1722	-	papB	99.7	98.4		(papB) regulatory protein PapB [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig00048	2127	2360	+	papI	100.0	94.9	NP_755468	(papI) regulatory protein PapI [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig00104	256	807	+	papX	100.0	97.6	NP_755457	(papX) PapX protein regulates flagellum synthesis to repress motility [P fimbriae (CVF425)] [Escherichia coli CFT073]
contig00048	18455	22354	+	sat	100.0	99.6	NP_755494	(sat) Aecreted auto transpoter toxin [Sat (VF0231)] [Escherichia coli CFT073]
contig00066	8392	9530	+	senB	99.9	99.7	YP_406304	(senB) enterotoxin [ShET2 (VF0258)] [Shigella flexneri 2a str. 301]
contig00005	225758	226511	+	yagV/ecpE	99.7	98.0	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00005	224191	225834	+	yagW/ecpD	100.0	99.2	NP_286007	(yagW/ecpD) polymerized tip adhesin of ECP fibers [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00005	221676	224201	+	yagX/ecpC	100.0	97.6	NP_286008	(yagX/ecpC) E. coli common pilus usher EcpC [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00005	220982	221650	+	yagY/ecpB	100.0	98.1	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00005	220338	220925	+	yagZ/ecpA	100.0	98.5	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00050	10665	11624	+	ybtA	100.0	99.3	NP_405473	(ybtA) transcriptional regulator YbtA [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00034	43654	45231	-	ybtE	100.0	99.8	NP_405468	(ybtE) yersiniabactin siderophore biosynthetic protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00050	8696	10498	-	ybtP	100.0	99.6	NP_405474	(ybtP) lipoprotein inner membrane ABC-transporter [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00050	6907	8709	-	ybtQ	100.0	99.6	NP_405475	(ybtQ) inner membrane ABC-transporter YbtQ [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00050	4302	5606	-	ybtS	100.0	99.8	NP_405477	(ybtS) salicylate synthase Irp9 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00034	45235	46038	-	ybtT	100.0	99.6	NP_405469	(ybtT) yersiniabactin biosynthetic protein YbtT [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00050	5634	6914	-	ybtX	100.0	99.7	NP_405476	(ybtX) putative signal transducer [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00005	219673	220263	+	ykgK/ecpR	100.0	99.5	NP_286011	(ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

ID177

Contig	Start	End	Strand	Gene	Coverage	Identity	Accession	Product
contig00018	53238	54666	+	aslA	100.0	97.1	AAG10151	(aslA) putative arylsulfatase [AslA (VF0238)] [Escherichia coli O18:K1:H7 str. RS218]
contig00010	36589	37617	-	chuS	100.0	96.4	NP_756169	(chuS) heme oxygenase ChuS [Chu (VF0227)] [Escherichia coli CFT073]
contig00010	43781	44773	+	chuU	100.0	96.6	NP_756179	(chuU) heme permease protein ChuU [Chu (VF0227)] [Escherichia coli CFT073]
contig00010	44740	45540	+	chuV	100.0	98.1	NP_756180	(chuV) ATP-binding hydrophilic protein ChuV [Chu (VF0227)] [Escherichia coli CFT073]
contig00010	41265	42602	+	chuW	100.0	96.8	NP_756176	(chuW) Putative oxygen independent coproporphyrinogen III oxidase [Chu (VF0227)] [Escherichia coli CFT073]
contig00010	43109	43732	+	chuY	100.0	96.5	NP_756178	(chuY) ChuY [Chu (VF0227)] [Escherichia coli CFT073]
contig00005	55718	56173	-	csgB	99.8	83.6	NP_460114	(csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00005	56928	57578	+	csgD	100.0	81.4	NP_460113	(csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00005	57997	58413	+	csgF	99.0	81.0	NP_460111	(csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00005	58440	59273	+	csgG	100.0	83.3	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00015	87858	88604	-	entA	100.0	97.3	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00015	88604	89461	-	entB	100.0	98.8	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00015	91095	92282	-	entC	100.0	97.3	NP_752611	(entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00015	106739	107509	+	entD	100.0	92.7	NP_752599	(entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00015	89475	91085	-	entE	100.0	96.5	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00015	98958	102811	-	entF	99.2	95.2	NP_752604	(entF) enterobactin synthase multienzyme complex component ATP-dependent [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00015	93419	94669	-	entS	100.0	95.7	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00003	220950	222848	-	espL1	100.0	96.3	NP_288154	(espL1) Type III secretion system effector espL1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00025	64706	66892	+	espL4	100.0	97.4	NP_290644	(espL4) Type III secretion system effector EspL4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00042	19883	21135	-	espR1	99.4	94.3	NP_287686	(espR1) Type III secretion system effector espR1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00003	14802	15941	+	espR3	100.0	94.7	NP_288394	(espR3) Type III secretion system effector espR3 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00003	12869	13978	+	espR4	97.3	84.4	NP_288396	(espR4) Type III secretion system effector espR4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00002	202198	203619	+	espX1	100.0	96.0	NP_285716	(espX1) Type III secretion system effector EspX1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00025	30844	32424	-	espX4	100.0	95.9	NP_290672	(espX4) Type III secretion system effector EspX4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00004	22900	24192	-	espX5	100.0	95.9	NP_290699	(espX5) Type III secretion system effector EspX5 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00002	162775	163511	-	espY1	97.9	93.9	NP_285753	(espY1) Type III secretion system effector EspY1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00002	145759	146309	-	espY2	96.5	88.8	NP_285765	(espY2) Type III secretion system effector EspY2 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00036	31222	32793	+	espY3	100.0	95.5	NP_286160	(espY3) Type III secretion system effector EspY3 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00024	39565	41973	+	espY4	100.0	96.4	NP_290352	(espY4) Type III secretion system effector EspY4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00009	106407	110657	-	fdeC	100.0	95.1	YP_002390132	(fdeC) adhesin FdeC [FdeC (VF0506)] [Escherichia coli O45:K1:H7 str. S88]
contig00015	104474	106714	+	fepA	100.0	96.9	NP_752600	(fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00015	92459	93415	+	fepB	100.0	97.7	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00015	96770	97585	+	fepC	100.0	96.9	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00015	94768	95784	+	fepD	100.0	96.0	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00015	95781	96773	+	fepG	100.0	94.2	NP_752607	(fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00015	103029	104231	-	fes	100.0	96.8	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00002	309512	310123	-	fimA	100.0	88.4	NP_757241	(fimA) Type-1 fimbrial protein A chain precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00002	311621	312223	-	fimB	100.0	98.0	NP_757239	(fimB) Type 1 fimbriae Regulatory protein fimB [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00002	308146	308871	-	fimC	100.0	98.5	NP_757243	(fimC) Chaperone protein fimC precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00002	305444	308079	-	fimD	100.0	98.5	NP_757244	(fimD) Outer membrane usher protein fimD precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00002	310550	311144	-	fimE	99.7	99.3	NP_757240	(fimE) Type 1 fimbriae Regulatory protein fimE [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00002	304904	305437	-	fimF	100.0	97.8	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00002	304388	304891	-	fimG	100.0	98.0	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00002	303466	304377	-	fimH	100.0	97.3	NP_757248	(fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00002	308908	309447	-	fimI	100.0	98.9	NP_757242	(fimI) Fimbrin-like protein fimI precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00007	37554	38384	-	gspC	100.0	95.3	YP_404599	(gspC) general secretion pathway protein C [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00007	35464	37314	-	gspD	100.0	96.2	YP_404600	(gspD) general secretion pathway protein D [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00007	33971	35464	-	gspE	100.0	95.3	YP_404601	(gspE) general secretion pathway protein E [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00007	32772	33971	-	gspF	100.0	95.0	YP_404602	(gspF) general secretion pathway protein F [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00007	32276	32731	-	gspG	100.0	95.4	YP_404603	(gspG) general secretion pathway protein G [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00007	31709	32239	-	gspH	100.0	95.3	YP_404604	(gspH) general secretion pathway protein H [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00007	31341	31712	-	gspI	100.0	95.2	YP_404605	(gspI) general secretion pathway protein I [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00007	30739	31308	-	gspJ	100.0	96.7	YP_404606	(gspJ) general secretion pathway protein J [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00007	29765	30742	-	gspK	100.0	96.5	YP_404607	(gspK) general secretion pathway protein K [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00007	28590	29450	-	gspL	100.0	95.9	YP_404608	(gspL) general secretion pathway protein L [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00007	28053	28474	-	gspM	99.8	94.5	YP_404609	(gspM) general secretion pathway protein M [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	291666	292028	+	gtrA	100.0	89.3	NP_706257	(gtrA) bactoprenol-linked glucose translocase/flippase [LPS (VF0124)] [Shigella flexneri 2a str. 301]
contig00001	292025	292933	+	gtrB	97.6	81.3	NP_706258	(gtrB) bactoprenol glucosyl transferase [LPS (VF0124)] [Shigella flexneri 2a str. 301]
contig00007	13223	14899	+	kpsD	100.0	98.1	AAA21682	(kpsD) KpsD [K1 capsule (VF0239)] [Escherichia coli O18:K1:H7 str. RS218]
contig00005	127746	128798	+	ompA	100.0	95.2	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00010	37666	39648	-	shuA	100.0	98.5	YP_405019	(shuA) outer membrane heme/hemoglobin receptor ShuA [Shu (VF0256)] [Shigella dysenteriae Sd197]
contig00010	40253	41245	+	shuT	100.0	98.1	YP_405017	(shuT) periplasmic binding protein ShuT [Shu (VF0256)] [Shigella dysenteriae Sd197]
contig00010	42615	43109	+	shuX	100.0	96.4	YP_405016	(shuX) shu locus protein ShuX [Shu (VF0256)] [Shigella dysenteriae Sd197]
contig00009	125988	126741	+	yagV/ecpE	99.7	97.9	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00009	124421	126064	+	yagW/ecpD	100.0	98.8	NP_286007	(yagW/ecpD) polymerized tip adhesin of ECP fibers [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00009	121906	124431	+	yagX/ecpC	100.0	98.0	NP_286008	(yagX/ecpC) E. coli common pilus usher EcpC [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00009	121212	121880	+	yagY/ecpB	100.0	97.5	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00009	120568	121155	+	yagZ/ecpA	100.0	99.0	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00009	119903	120493	+	ykgK/ecpR	100.0	99.0	NP_286011	(ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

ID178

Contig	Start	End	Strand	Gene	Coverage	Identity	Accession	Product
contig00016	67237	68665	+	aslA	100.0	97.4	AAG10151	(aslA) putative arylsulfatase [AslA (VF0238)] [Escherichia coli O18:K1:H7 str. RS218]
contig00008	176914	177942	-	chuS	100.0	98.0	NP_756169	(chuS) heme oxygenase ChuS [Chu (VF0227)] [Escherichia coli CFT073]
contig00008	180579	181571	+	chuT	100.0	99.4	NP_756175	(chuT) periplasmic heme-binding protein ChuT [Chu (VF0227)] [Escherichia coli CFT073]
contig00008	184107	185099	+	chuU	100.0	99.1	NP_756179	(chuU) heme permease protein ChuU [Chu (VF0227)] [Escherichia coli CFT073]
contig00008	185066	185866	+	chuV	100.0	98.4	NP_756180	(chuV) ATP-binding hydrophilic protein ChuV [Chu (VF0227)] [Escherichia coli CFT073]
contig00008	181591	182928	+	chuW	100.0	97.9	NP_756176	(chuW) Putative oxygen independent coproporphyrinogen III oxidase [Chu (VF0227)] [Escherichia coli CFT073]
contig00008	183435	184058	+	chuY	100.0	96.3	NP_756178	(chuY) ChuY [Chu (VF0227)] [Escherichia coli CFT073]
contig00007	175787	176242	+	csgB	99.8	83.8	NP_460114	(csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00007	174381	175031	-	csgD	100.0	81.3	NP_460113	(csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00007	173546	173962	-	csgF	99.0	81.2	NP_460111	(csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00007	172686	173519	-	csgG	100.0	83.0	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00019	19648	20394	-	entA	100.0	96.4	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00019	20394	21251	-	entB	100.0	98.2	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00019	22885	24072	-	entC	100.0	98.4	NP_752611	(entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00019	38529	39299	+	entD	100.0	93.9	NP_752599	(entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00019	21265	22875	-	entE	100.0	96.5	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00019	30748	34601	-	entF	99.3	96.3	NP_752604	(entF) enterobactin synthase multienzyme complex component ATP-dependent [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00019	25209	26459	-	entS	100.0	96.3	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00002	198777	200675	-	espL1	100.0	96.0	NP_288154	(espL1) Type III secretion system effector espL1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00022	49101	50351	+	espR1	99.3	94.7	NP_287686	(espR1) Type III secretion system effector espR1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00025	20282	21390	-	espR4	97.2	84.4	NP_288396	(espR4) Type III secretion system effector espR4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00004	203188	204609	+	espX1	100.0	93.2	NP_285716	(espX1) Type III secretion system effector EspX1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00009	57205	58785	+	espX4	100.0	96.0	NP_290672	(espX4) Type III secretion system effector EspX4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00004	163720	164468	-	espY1	99.5	94.4	NP_285753	(espY1) Type III secretion system effector EspY1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00004	146689	147258	-	espY2	100.0	93.9	NP_285765	(espY2) Type III secretion system effector EspY2 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00015	44939	47347	+	espY4	99.8	89.4	NP_290352	(espY4) Type III secretion system effector EspY4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00006	255018	259259	-	fdeC	99.8	92.0	YP_002390132	(fdeC) adhesin FdeC [FdeC (VF0506)] [Escherichia coli O45:K1:H7 str. S88]
contig00019	36264	38504	+	fepA	100.0	97.9	NP_752600	(fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00019	24249	25205	+	fepB	100.0	98.2	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00019	28560	29375	+	fepC	100.0	97.7	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00019	26558	27574	+	fepD	100.0	96.5	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00019	27571	28563	+	fepG	100.0	94.5	NP_752607	(fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00019	34819	36021	-	fes	100.0	97.0	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00020	38238	40259	+	fyuA	100.0	99.8	NP_405467	(fyuA) pesticin/yersiniabactin receptor protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00026	33848	34678	+	gspC	100.0	95.1	YP_404599	(gspC) general secretion pathway protein C [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00026	34918	36768	+	gspD	100.0	96.1	YP_404600	(gspD) general secretion pathway protein D [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00026	36768	38261	+	gspE	100.0	94.6	YP_404601	(gspE) general secretion pathway protein E [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00026	38261	39460	+	gspF	100.0	94.3	YP_404602	(gspF) general secretion pathway protein F [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00026	39501	39956	+	gspG	100.0	96.7	YP_404603	(gspG) general secretion pathway protein G [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00026	39993	40523	+	gspH	100.0	97.2	YP_404604	(gspH) general secretion pathway protein H [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00026	40520	40891	+	gspI	100.0	95.2	YP_404605	(gspI) general secretion pathway protein I [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00026	40924	41493	+	gspJ	100.0	96.3	YP_404606	(gspJ) general secretion pathway protein J [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00026	41490	42467	+	gspK	100.0	97.2	YP_404607	(gspK) general secretion pathway protein K [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00026	42782	43642	+	gspL	100.0	94.9	YP_404608	(gspL) general secretion pathway protein L [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00026	43758	44179	+	gspM	99.8	95.7	YP_404609	(gspM) general secretion pathway protein M [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00020	25138	34629	+	irp1	100.0	99.2	NP_405471	(irp1) yersiniabactin biosynthetic protein Irp1 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00020	18943	25050	+	irp2	100.0	99.8	NP_405472	(irp2) yersiniabactin biosynthetic protein Irp2 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00046	7018	8805	+	iucA	100.0	94.3	NP_755502	(iucA) aerobactin siderophore biosynthesis protein IucD [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00046	8806	9752	+	iucB	99.9	95.7	NP_755501	(iucB) aerobactin siderophore biosynthesis protein IucB [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00046	9752	11494	+	iucC	100.0	96.1	NP_755500	(iucC) aerobactin siderophore biosynthesis protein IucC [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00046	11491	12812	+	iucD	98.8	96.3	NP_755499	(iucD) L-lysine 6-monooxygenase IucD [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00046	12750	15051	+	iutA	100.0	88.4	NP_755498	(iutA) ferric aerobactin receptor precusor IutA [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00023	53381	55057	+	kpsD	100.0	97.9	AAA21682	(kpsD) KpsD [K1 capsule (VF0239)] [Escherichia coli O18:K1:H7 str. RS218]
contig00026	45241	46017	+	kpsM	100.0	92.7	AAA24046	(kpsM) KpsM [K1 capsule (VF0239)] [Escherichia coli O18:K1:H7 str. RS218]
contig00007	103621	104661	-	ompA	100.0	98.1	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00084	958	1509	+	papX	100.0	97.5	NP_755457	(papX) PapX protein regulates flagellum synthesis to repress motility [P fimbriae (CVF425)] [Escherichia coli CFT073]
contig00008	177991	179973	-	shuA	100.0	98.0	YP_405019	(shuA) outer membrane heme/hemoglobin receptor ShuA [Shu (VF0256)] [Shigella dysenteriae Sd197]
contig00008	182941	183435	+	shuX	100.0	96.6	YP_405016	(shuX) shu locus protein ShuX [Shu (VF0256)] [Shigella dysenteriae Sd197]
contig00006	274671	275424	+	yagV/ecpE	99.7	98.1	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00006	273104	274747	+	yagW/ecpD	100.0	99.1	NP_286007	(yagW/ecpD) polymerized tip adhesin of ECP fibers [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00006	270589	273114	+	yagX/ecpC	100.0	98.5	NP_286008	(yagX/ecpC) E. coli common pilus usher EcpC [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00006	269895	270563	+	yagY/ecpB	100.0	99.0	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00006	269250	269837	+	yagZ/ecpA	100.0	99.0	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00020	17793	18752	+	ybtA	100.0	99.5	NP_405473	(ybtA) transcriptional regulator YbtA [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00020	36530	38107	+	ybtE	100.0	99.9	NP_405468	(ybtE) yersiniabactin siderophore biosynthetic protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00020	15824	17626	-	ybtP	100.0	99.7	NP_405474	(ybtP) lipoprotein inner membrane ABC-transporter [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00020	14035	15837	-	ybtQ	100.0	99.7	NP_405475	(ybtQ) inner membrane ABC-transporter YbtQ [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00020	11430	12734	-	ybtS	100.0	99.7	NP_405477	(ybtS) salicylate synthase Irp9 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00020	35723	36526	+	ybtT	100.0	99.6	NP_405469	(ybtT) yersiniabactin biosynthetic protein YbtT [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00020	34626	35726	+	ybtU	100.0	99.7	NP_405470	(ybtU) yersiniabactin biosynthetic protein YbtU [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00020	12762	14042	-	ybtX	100.0	99.7	NP_405476	(ybtX) putative signal transducer [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00006	268585	269175	+	ykgK/ecpR	100.0	99.7	NP_286011	(ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

ID182

Contig	Start	End	Strand	Gene	Coverage	Identity	Accession	Product
contig00030	16559	17986	+	aslA	99.9	93.5	AAG10151	(aslA) putative arylsulfatase [AslA (VF0238)] [Escherichia coli O18:K1:H7 str. RS218]
contig00055	1	789	+	csgG	94.6	83.5	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00008	96808	97554	-	entA	100.0	95.7	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00008	97554	98411	-	entB	100.0	98.1	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00008	100045	101232	-	entC	100.0	97.8	NP_752611	(entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00008	115876	116646	+	entD	100.0	94.3	NP_752599	(entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00008	98425	100035	-	entE	100.0	95.5	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00008	108095	111948	-	entF	99.3	95.6	NP_752604	(entF) enterobactin synthase multienzyme complex component ATP-dependent [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00008	102555	103805	-	entS	100.0	95.4	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00040	13782	15681	-	espL1	100.0	97.5	NP_288154	(espL1) Type III secretion system effector espL1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00062	7453	8508	+	espR1	83.7	93.8	NP_287686	(espR1) Type III secretion system effector espR1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00053	6006	7298	-	espX5	100.0	96.6	NP_290699	(espX5) Type III secretion system effector EspX5 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00079	3412	7660	-	fdeC	99.9	94.2	YP_002390132	(fdeC) adhesin FdeC [FdeC (VF0506)] [Escherichia coli O45:K1:H7 str. S88]
contig00008	113611	115851	+	fepA	100.0	96.8	NP_752600	(fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00008	101595	102551	+	fepB	100.0	97.5	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00008	105906	106721	+	fepC	100.0	97.3	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00008	103904	104920	+	fepD	100.0	96.1	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00008	104917	105909	+	fepG	100.0	94.1	NP_752607	(fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00008	112166	113368	-	fes	100.0	96.7	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00010	94747	95358	-	fimA	100.0	88.4	NP_757241	(fimA) Type-1 fimbrial protein A chain precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00010	96856	97458	-	fimB	100.0	97.7	NP_757239	(fimB) Type 1 fimbriae Regulatory protein fimB [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00010	93381	94106	-	fimC	100.0	98.5	NP_757243	(fimC) Chaperone protein fimC precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00010	90678	93314	-	fimD	100.0	98.5	NP_757244	(fimD) Outer membrane usher protein fimD precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00010	95785	96379	-	fimE	99.7	99.2	NP_757240	(fimE) Type 1 fimbriae Regulatory protein fimE [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00010	90138	90671	-	fimF	100.0	97.6	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00010	89622	90125	-	fimG	100.0	98.0	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00010	88700	89611	-	fimH	100.0	97.3	NP_757248	(fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00010	94143	94682	-	fimI	100.0	98.7	NP_757242	(fimI) Fimbrin-like protein fimI precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00028	17917	18747	+	gspC	100.0	95.3	YP_404599	(gspC) general secretion pathway protein C [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00028	18987	20837	+	gspD	100.0	97.1	YP_404600	(gspD) general secretion pathway protein D [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00028	20837	22330	+	gspE	100.0	96.5	YP_404601	(gspE) general secretion pathway protein E [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00028	22330	23529	+	gspF	100.0	96.2	YP_404602	(gspF) general secretion pathway protein F [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00028	23570	24025	+	gspG	100.0	95.0	YP_404603	(gspG) general secretion pathway protein G [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00028	24062	24592	+	gspH	100.0	95.5	YP_404604	(gspH) general secretion pathway protein H [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00028	24589	24960	+	gspI	100.0	95.2	YP_404605	(gspI) general secretion pathway protein I [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00028	24993	25562	+	gspJ	100.0	96.7	YP_404606	(gspJ) general secretion pathway protein J [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00028	25559	26536	+	gspK	100.0	97.0	YP_404607	(gspK) general secretion pathway protein K [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00028	26851	27711	+	gspL	100.0	97.1	YP_404608	(gspL) general secretion pathway protein L [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00028	27827	28249	+	gspM	100.0	98.3	YP_404609	(gspM) general secretion pathway protein M [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00004	81123	82448	+	nleA/espI	100.0	97.8	NP_287961	(nleA/espI) Type III secretion system effector NleA [NleA/EspI (VF0338)] [Escherichia coli O157:H7 str. EDL933]
contig00027	19444	20484	-	ompA	100.0	98.1	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00089	5956	6709	+	yagV/ecpE	99.7	97.0	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00089	4389	6032	+	yagW/ecpD	100.0	99.1	NP_286007	(yagW/ecpD) polymerized tip adhesin of ECP fibers [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00089	1874	4399	+	yagX/ecpC	100.0	98.7	NP_286008	(yagX/ecpC) E. coli common pilus usher EcpC [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00089	1180	1848	+	yagY/ecpB	100.0	98.1	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00089	534	1122	+	yagZ/ecpA	100.0	99.0	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

ID186

Contig	Start	End	Strand	Gene	Coverage	Identity	Accession	Product
contig00003	178176	178631	+	csgB	99.8	84.0	NP_460114	(csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00003	176772	177422	-	csgD	100.0	81.1	NP_460113	(csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00003	175937	176353	-	csgF	99.0	81.2	NP_460111	(csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00003	175077	175910	-	csgG	100.0	83.1	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00007	99596	100342	-	entA	100.0	96.0	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00007	100342	101199	-	entB	100.0	97.9	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00007	102833	104020	-	entC	100.0	97.5	NP_752611	(entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00007	118664	119434	+	entD	100.0	94.0	NP_752599	(entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00007	101213	102823	-	entE	100.0	95.8	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00007	110907	114736	-	entF	98.7	95.4	NP_752604	(entF) enterobactin synthase multienzyme complex component ATP-dependent [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00007	105343	106593	-	entS	100.0	95.6	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00009	74456	76324	-	espL1	98.4	95.3	NP_288154	(espL1) Type III secretion system effector espL1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00033	24866	25921	+	espR1	83.8	94.2	NP_287686	(espR1) Type III secretion system effector espR1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00011	142372	143792	+	espX1	99.9	94.7	NP_285716	(espX1) Type III secretion system effector EspX1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00013	39590	41170	+	espX4	99.9	93.1	NP_290672	(espX4) Type III secretion system effector EspX4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00013	70690	71982	-	espX5	100.0	95.7	NP_290699	(espX5) Type III secretion system effector EspX5 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00016	43044	47285	-	fdeC	99.8	92.4	YP_002390132	(fdeC) adhesin FdeC [FdeC (VF0506)] [Escherichia coli O45:K1:H7 str. S88]
contig00007	116399	118639	+	fepA	100.0	96.8	NP_752600	(fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00007	104383	105339	+	fepB	100.0	97.4	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00007	108694	109509	+	fepC	100.0	97.3	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00007	106692	107708	+	fepD	100.0	96.0	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00007	107705	108697	+	fepG	100.0	94.0	NP_752607	(fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00007	114954	116156	-	fes	100.0	96.8	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00018	97591	98196	-	fimA	100.0	92.2	NP_757241	(fimA) Type-1 fimbrial protein A chain precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00040	1112	1714	-	fimB	100.0	98.2	NP_757239	(fimB) Type 1 fimbriae Regulatory protein fimB [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00018	96225	96950	-	fimC	100.0	98.5	NP_757243	(fimC) Chaperone protein fimC precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00018	93522	96158	-	fimD	100.0	98.3	NP_757244	(fimD) Outer membrane usher protein fimD precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00040	38	634	-	fimE	100.0	98.7	NP_757240	(fimE) Type 1 fimbriae Regulatory protein fimE [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00018	92982	93515	-	fimF	100.0	97.4	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00018	92466	92969	-	fimG	100.0	98.0	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00018	91544	92455	-	fimH	100.0	97.3	NP_757248	(fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00018	96987	97526	-	fimI	100.0	98.3	NP_757242	(fimI) Fimbrin-like protein fimI precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00001	353256	354086	-	gspC	100.0	95.1	YP_404599	(gspC) general secretion pathway protein C [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	351166	353016	-	gspD	100.0	97.0	YP_404600	(gspD) general secretion pathway protein D [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	349673	351166	-	gspE	100.0	97.1	YP_404601	(gspE) general secretion pathway protein E [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	348474	349673	-	gspF	100.0	96.2	YP_404602	(gspF) general secretion pathway protein F [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	347978	348433	-	gspG	100.0	95.6	YP_404603	(gspG) general secretion pathway protein G [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	347411	347941	-	gspH	100.0	96.0	YP_404604	(gspH) general secretion pathway protein H [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	347043	347414	-	gspI	100.0	95.2	YP_404605	(gspI) general secretion pathway protein I [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	346441	347010	-	gspJ	100.0	97.2	YP_404606	(gspJ) general secretion pathway protein J [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	345467	346444	-	gspK	100.0	96.1	YP_404607	(gspK) general secretion pathway protein K [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	344292	345152	-	gspL	100.0	97.6	YP_404608	(gspL) general secretion pathway protein L [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	343754	344176	-	gspM	100.0	94.1	YP_404609	(gspM) general secretion pathway protein M [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00047	1792	2954	+	iroB	99.9	98.4	NP_753168	(iroB) glucosyltransferase IroB [Salmochelin (IA013)] [Escherichia coli CFT073]
contig00047	3017	6754	+	iroC	100.0	99.2	NP_753167	(iroC) ATP binding cassette transporter [Salmochelin (IA013)] [Escherichia coli CFT073]
contig00047	6858	8087	+	iroD	100.0	98.9	NP_753166	(iroD) esterase [Salmochelin (IA013)] [Escherichia coli CFT073]
contig00047	8172	9128	+	iroE	100.0	99.5	NP_753165	(iroE) esterase [Salmochelin (IA013)] [Escherichia coli CFT073]
contig00047	9173	11350	-	iroN	100.0	99.1	NP_753164	(iroN) salmochelin receptor IroN [IroN (VF0230)] [Escherichia coli CFT073]
contig00003	104209	105261	-	ompA	100.0	94.3	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00016	56391	57144	+	yagV/ecpE	99.7	96.8	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00016	54824	56467	+	yagW/ecpD	100.0	98.6	NP_286007	(yagW/ecpD) polymerized tip adhesin of ECP fibers [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00016	52309	54834	+	yagX/ecpC	100.0	98.7	NP_286008	(yagX/ecpC) E. coli common pilus usher EcpC [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00016	51615	52283	+	yagY/ecpB	100.0	98.7	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00016	50970	51557	+	yagZ/ecpA	100.0	99.3	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00016	50305	50895	+	ykgK/ecpR	100.0	97.6	NP_286011	(ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

ID187

Contig	Start	End	Strand	Gene	Coverage	Identity	Accession	Product
contig00036	14792	16220	+	aslA	100.0	97.1	AAG10151	(aslA) putative arylsulfatase [AslA (VF0238)] [Escherichia coli O18:K1:H7 str. RS218]
contig00018	1	437	+	csgB	95.6	82.7	NP_460114	(csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00085	355	1188	+	csgG	100.0	83.5	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00013	99269	100015	-	entA	100.0	95.7	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00013	100015	100872	-	entB	100.0	98.1	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00013	102506	103693	-	entC	100.0	97.9	NP_752611	(entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00013	118337	119107	+	entD	100.0	95.2	NP_752599	(entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00013	100886	102496	-	entE	100.0	95.5	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00013	110556	114409	-	entF	99.3	95.7	NP_752604	(entF) enterobactin synthase multienzyme complex component ATP-dependent [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00013	105016	106266	-	entS	100.0	95.4	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00003	157262	159160	-	espL1	100.0	96.3	NP_288154	(espL1) Type III secretion system effector espL1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00022	73346	75532	+	espL4	100.0	97.3	NP_290644	(espL4) Type III secretion system effector EspL4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00040	25720	26774	+	espR1	83.7	93.9	NP_287686	(espR1) Type III secretion system effector espR1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00022	43550	45130	-	espX4	99.9	93.4	NP_290672	(espX4) Type III secretion system effector EspX4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00022	12759	14051	+	espX5	100.0	97.1	NP_290699	(espX5) Type III secretion system effector EspX5 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00013	116072	118312	+	fepA	100.0	96.7	NP_752600	(fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00013	104056	105012	+	fepB	100.0	97.5	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00013	108367	109182	+	fepC	100.0	97.2	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00013	106365	107381	+	fepD	100.0	96.1	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00013	107378	108370	+	fepG	100.0	94.1	NP_752607	(fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00013	114627	115829	-	fes	100.0	96.7	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00069	7943	8476	-	fimF	100.0	97.8	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00069	7427	7930	-	fimG	100.0	98.0	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00069	6504	7416	-	fimH	100.0	97.0	NP_757248	(fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00002	99656	100516	-	gspL	100.0	97.1	YP_404608	(gspL) general secretion pathway protein L [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00002	99118	99540	-	gspM	100.0	98.3	YP_404609	(gspM) general secretion pathway protein M [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00009	73772	74824	-	ompA	100.0	94.4	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00001	224412	225165	+	yagV/ecpE	99.7	97.0	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00001	222845	224488	+	yagW/ecpD	100.0	99.0	NP_286007	(yagW/ecpD) polymerized tip adhesin of ECP fibers [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00001	220330	222855	+	yagX/ecpC	100.0	98.8	NP_286008	(yagX/ecpC) E. coli common pilus usher EcpC [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00001	219636	220304	+	yagY/ecpB	100.0	97.9	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00001	218991	219578	+	yagZ/ecpA	100.0	99.2	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00001	218326	218916	+	ykgK/ecpR	100.0	97.0	NP_286011	(ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

ID195

Contig	Start	End	Strand	Gene	Coverage	Identity	Accession	Product
contig00006	167361	167816	-	csgB	99.8	83.8	NP_460114	(csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00006	168570	169220	+	csgD	100.0	81.1	NP_460113	(csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00006	169639	170055	+	csgF	99.0	81.2	NP_460111	(csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00006	170082	170915	+	csgG	100.0	83.1	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00012	99363	100109	-	entA	100.0	96.0	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00012	100109	100966	-	entB	100.0	98.0	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00012	102600	103787	-	entC	100.0	97.6	NP_752611	(entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00012	118432	119202	+	entD	100.0	93.9	NP_752599	(entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00012	100980	102590	-	entE	100.0	96.2	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00012	110675	114504	-	entF	98.7	95.9	NP_752604	(entF) enterobactin synthase multienzyme complex component ATP-dependent [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00012	105110	106360	-	entS	100.0	95.6	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00002	245552	247450	-	espL1	100.0	94.9	NP_288154	(espL1) Type III secretion system effector espL1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00017	11593	12648	-	espR1	83.8	94.1	NP_287686	(espR1) Type III secretion system effector espR1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00035	18843	20263	+	espX1	99.9	94.3	NP_285716	(espX1) Type III secretion system effector EspX1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00020	55502	57083	-	espX4	99.9	92.9	NP_290672	(espX4) Type III secretion system effector EspX4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00020	24684	25976	+	espX5	100.0	95.5	NP_290699	(espX5) Type III secretion system effector EspX5 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00009	131886	136111	-	fdeC	99.4	91.8	YP_002390132	(fdeC) adhesin FdeC [FdeC (VF0506)] [Escherichia coli O45:K1:H7 str. S88]
contig00012	116167	118407	+	fepA	100.0	96.8	NP_752600	(fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00012	104150	105106	+	fepB	100.0	97.4	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00012	108461	109276	+	fepC	100.0	97.2	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00012	106459	107475	+	fepD	100.0	96.3	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00012	107472	108464	+	fepG	100.0	94.8	NP_752607	(fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00012	114722	115924	-	fes	100.0	96.5	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00019	100460	101064	-	fimA	99.8	90.6	NP_757241	(fimA) Type-1 fimbrial protein A chain precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00031	1111	1713	-	fimB	100.0	98.0	NP_757239	(fimB) Type 1 fimbriae Regulatory protein fimB [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00019	99094	99819	-	fimC	100.0	98.3	NP_757243	(fimC) Chaperone protein fimC precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00019	96391	99027	-	fimD	100.0	98.8	NP_757244	(fimD) Outer membrane usher protein fimD precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00031	37	633	-	fimE	100.0	98.5	NP_757240	(fimE) Type 1 fimbriae Regulatory protein fimE [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00019	95851	96384	-	fimF	100.0	97.0	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00019	95335	95838	-	fimG	100.0	97.8	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00019	94413	95324	-	fimH	100.0	97.3	NP_757248	(fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00019	99856	100395	-	fimI	100.0	98.7	NP_757242	(fimI) Fimbrin-like protein fimI precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00008	33909	34739	+	gspC	100.0	95.1	YP_404599	(gspC) general secretion pathway protein C [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00008	34979	36829	+	gspD	100.0	97.2	YP_404600	(gspD) general secretion pathway protein D [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00008	36829	38322	+	gspE	100.0	96.8	YP_404601	(gspE) general secretion pathway protein E [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00008	38322	39521	+	gspF	100.0	96.2	YP_404602	(gspF) general secretion pathway protein F [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00008	39562	40017	+	gspG	100.0	95.6	YP_404603	(gspG) general secretion pathway protein G [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00008	40054	40584	+	gspH	100.0	95.9	YP_404604	(gspH) general secretion pathway protein H [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00008	40581	40952	+	gspI	100.0	94.6	YP_404605	(gspI) general secretion pathway protein I [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00008	40985	41554	+	gspJ	100.0	97.2	YP_404606	(gspJ) general secretion pathway protein J [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00008	41551	42528	+	gspK	100.0	97.8	YP_404607	(gspK) general secretion pathway protein K [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00008	42843	43703	+	gspL	100.0	97.6	YP_404608	(gspL) general secretion pathway protein L [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00008	43819	44241	+	gspM	100.0	94.1	YP_404609	(gspM) general secretion pathway protein M [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00005	104054	105106	-	ompA	100.0	94.2	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00009	145195	145948	+	yagV/ecpE	99.7	96.8	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00009	143628	145271	+	yagW/ecpD	100.0	98.7	NP_286007	(yagW/ecpD) polymerized tip adhesin of ECP fibers [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00009	141113	143638	+	yagX/ecpC	100.0	98.7	NP_286008	(yagX/ecpC) E. coli common pilus usher EcpC [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00009	140419	141087	+	yagY/ecpB	100.0	98.2	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00009	139775	140362	+	yagZ/ecpA	100.0	99.3	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00009	139110	139700	+	ykgK/ecpR	100.0	97.6	NP_286011	(ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

ID197

Contig	Start	End	Strand	Gene	Coverage	Identity	Accession	Product
contig00022	49279	50707	+	aslA	100.0	93.6	AAG10151	(aslA) putative arylsulfatase [AslA (VF0238)] [Escherichia coli O18:K1:H7 str. RS218]
contig00035	6296	6751	+	csgB	99.8	83.8	NP_460114	(csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00035	4891	5541	-	csgD	100.0	81.1	NP_460113	(csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00035	4056	4472	-	csgF	99.0	81.2	NP_460111	(csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00035	3196	4029	-	csgG	100.0	83.5	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00015	99075	99821	-	entA	100.0	95.7	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00015	99821	100678	-	entB	100.0	98.0	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00015	102312	103499	-	entC	100.0	97.9	NP_752611	(entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00015	118143	118913	+	entD	100.0	95.2	NP_752599	(entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00015	100692	102302	-	entE	100.0	95.5	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00015	110362	114215	-	entF	99.3	95.7	NP_752604	(entF) enterobactin synthase multienzyme complex component ATP-dependent [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00015	104822	106072	-	entS	100.0	95.4	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00025	11801	13700	+	espL1	100.0	97.6	NP_288154	(espL1) Type III secretion system effector espL1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00050	19358	21544	+	espL4	100.0	97.3	NP_290644	(espL4) Type III secretion system effector EspL4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00041	25445	26498	+	espR1	83.7	93.8	NP_287686	(espR1) Type III secretion system effector espR1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00016	98648	99783	-	espR4	99.6	84.4	NP_288396	(espR4) Type III secretion system effector espR4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00007	144231	145652	+	espX1	100.0	95.2	NP_285716	(espX1) Type III secretion system effector EspX1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00006	164243	165823	-	espX4	99.9	93.3	NP_290672	(espX4) Type III secretion system effector EspX4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00006	133452	134744	+	espX5	100.0	97.1	NP_290699	(espX5) Type III secretion system effector EspX5 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00007	105276	106087	-	espY1	99.9	87.0	NP_285753	(espY1) Type III secretion system effector EspY1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00039	20571	24819	-	fdeC	99.9	94.2	YP_002390132	(fdeC) adhesin FdeC [FdeC (VF0506)] [Escherichia coli O45:K1:H7 str. S88]
contig00015	115878	118118	+	fepA	100.0	96.7	NP_752600	(fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00015	103862	104818	+	fepB	100.0	97.5	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00015	108173	108988	+	fepC	100.0	97.3	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00015	106171	107187	+	fepD	100.0	96.1	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00015	107184	108176	+	fepG	100.0	94.1	NP_752607	(fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00015	114433	115635	-	fes	100.0	96.7	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00027	46362	48383	-	fyuA	100.0	100.0	NP_405467	(fyuA) pesticin/yersiniabactin receptor protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00027	51992	61483	-	irp1	100.0	99.8	NP_405471	(irp1) yersiniabactin biosynthetic protein Irp1 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00027	61571	67678	-	irp2	100.0	99.8	NP_405472	(irp2) yersiniabactin biosynthetic protein Irp2 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00055	7016	8803	+	iucA	100.0	94.2	NP_755502	(iucA) aerobactin siderophore biosynthesis protein IucD [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00055	8804	9751	+	iucB	100.0	95.6	NP_755501	(iucB) aerobactin siderophore biosynthesis protein IucB [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00055	9751	11493	+	iucC	100.0	96.0	NP_755500	(iucC) aerobactin siderophore biosynthesis protein IucC [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00055	11490	12811	+	iucD	98.8	96.3	NP_755499	(iucD) L-lysine 6-monooxygenase IucD [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00055	12749	15050	+	iutA	100.0	88.4	NP_755498	(iutA) ferric aerobactin receptor precusor IutA [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00001	282779	283819	-	ompA	100.0	98.1	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00039	33926	34679	+	yagV/ecpE	99.7	97.1	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00039	32359	34002	+	yagW/ecpD	100.0	99.1	NP_286007	(yagW/ecpD) polymerized tip adhesin of ECP fibers [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00039	29844	32369	+	yagX/ecpC	100.0	98.8	NP_286008	(yagX/ecpC) E. coli common pilus usher EcpC [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00039	29150	29818	+	yagY/ecpB	100.0	98.1	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00039	28505	29092	+	yagZ/ecpA	100.0	99.2	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00027	67869	68828	-	ybtA	100.0	99.9	NP_405473	(ybtA) transcriptional regulator YbtA [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00027	48514	50091	-	ybtE	100.0	99.8	NP_405468	(ybtE) yersiniabactin siderophore biosynthetic protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00027	68995	70797	+	ybtP	100.0	99.6	NP_405474	(ybtP) lipoprotein inner membrane ABC-transporter [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00027	70784	72586	+	ybtQ	100.0	99.8	NP_405475	(ybtQ) inner membrane ABC-transporter YbtQ [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00027	73887	75191	+	ybtS	100.0	97.6	NP_405477	(ybtS) salicylate synthase Irp9 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00027	50095	50898	-	ybtT	100.0	99.8	NP_405469	(ybtT) yersiniabactin biosynthetic protein YbtT [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00027	50895	51995	-	ybtU	100.0	99.7	NP_405470	(ybtU) yersiniabactin biosynthetic protein YbtU [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00027	72579	73859	+	ybtX	100.0	97.6	NP_405476	(ybtX) putative signal transducer [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00039	27840	28430	+	ykgK/ecpR	100.0	96.8	NP_286011	(ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

ID199

Contig	Start	End	Strand	Gene	Coverage	Identity	Accession	Product
contig00002	390237	390692	-	csgB	99.8	83.8	NP_460114	(csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00002	391446	392096	+	csgD	100.0	81.1	NP_460113	(csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00002	392515	392931	+	csgF	99.0	81.2	NP_460111	(csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00002	392958	393791	+	csgG	100.0	83.0	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00004	99473	100219	-	entA	100.0	95.5	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00004	100219	101076	-	entB	100.0	97.4	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00004	102710	103897	-	entC	100.0	97.6	NP_752611	(entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00004	118541	119311	+	entD	100.0	94.3	NP_752599	(entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00004	101090	102700	-	entE	100.0	95.8	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00004	110784	114613	-	entF	98.7	95.4	NP_752604	(entF) enterobactin synthase multienzyme complex component ATP-dependent [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00004	105220	106470	-	entS	100.0	95.6	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00005	67814	69713	-	espL1	100.0	95.7	NP_288154	(espL1) Type III secretion system effector espL1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00026	25018	26073	+	espR1	83.8	94.1	NP_287686	(espR1) Type III secretion system effector espR1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00003	200456	201876	+	espX1	99.9	95.7	NP_285716	(espX1) Type III secretion system effector EspX1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00014	55586	57166	-	espX4	99.9	93.0	NP_290672	(espX4) Type III secretion system effector EspX4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00014	24737	26029	+	espX5	100.0	95.9	NP_290699	(espX5) Type III secretion system effector EspX5 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00022	33490	37738	-	fdeC	99.9	94.2	YP_002390132	(fdeC) adhesin FdeC [FdeC (VF0506)] [Escherichia coli O45:K1:H7 str. S88]
contig00004	116276	118516	+	fepA	100.0	97.1	NP_752600	(fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00004	104260	105216	+	fepB	100.0	97.1	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00004	108571	109386	+	fepC	100.0	97.2	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00004	106569	107585	+	fepD	100.0	96.0	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00004	107582	108574	+	fepG	100.0	94.0	NP_752607	(fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00004	114831	116033	-	fes	100.0	96.5	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00003	323693	324298	-	fimA	100.0	92.9	NP_757241	(fimA) Type-1 fimbrial protein A chain precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00003	325796	326398	-	fimB	100.0	98.0	NP_757239	(fimB) Type 1 fimbriae Regulatory protein fimB [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00003	322327	323052	-	fimC	100.0	98.3	NP_757243	(fimC) Chaperone protein fimC precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00003	319624	322260	-	fimD	100.0	98.6	NP_757244	(fimD) Outer membrane usher protein fimD precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00003	324722	325318	-	fimE	100.0	98.7	NP_757240	(fimE) Type 1 fimbriae Regulatory protein fimE [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00003	319084	319617	-	fimF	100.0	98.3	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00003	318568	319071	-	fimG	100.0	98.2	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00003	317646	318557	-	fimH	100.0	97.4	NP_757248	(fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00003	323089	323628	-	fimI	100.0	99.1	NP_757242	(fimI) Fimbrin-like protein fimI precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00009	35153	37174	-	fyuA	100.0	99.9	NP_405467	(fyuA) pesticin/yersiniabactin receptor protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00001	314032	314862	+	gspC	100.0	95.2	YP_404599	(gspC) general secretion pathway protein C [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	315102	316952	+	gspD	100.0	97.1	YP_404600	(gspD) general secretion pathway protein D [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	316952	318445	+	gspE	100.0	96.0	YP_404601	(gspE) general secretion pathway protein E [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	318445	319644	+	gspF	100.0	96.2	YP_404602	(gspF) general secretion pathway protein F [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	319685	320140	+	gspG	100.0	95.6	YP_404603	(gspG) general secretion pathway protein G [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	320177	320707	+	gspH	100.0	96.0	YP_404604	(gspH) general secretion pathway protein H [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	320704	321075	+	gspI	100.0	95.2	YP_404605	(gspI) general secretion pathway protein I [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	321108	321677	+	gspJ	100.0	97.2	YP_404606	(gspJ) general secretion pathway protein J [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	321674	322651	+	gspK	100.0	97.8	YP_404607	(gspK) general secretion pathway protein K [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	322966	323826	+	gspL	100.0	97.3	YP_404608	(gspL) general secretion pathway protein L [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	323942	324364	+	gspM	100.0	95.0	YP_404609	(gspM) general secretion pathway protein M [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00009	40784	50275	-	irp1	100.0	99.7	NP_405471	(irp1) yersiniabactin biosynthetic protein Irp1 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00009	50363	56470	-	irp2	100.0	99.5	NP_405472	(irp2) yersiniabactin biosynthetic protein Irp2 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00017	77080	78132	-	ompA	100.0	94.3	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00022	46844	47597	+	yagV/ecpE	99.7	96.8	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00022	45277	46920	+	yagW/ecpD	100.0	98.7	NP_286007	(yagW/ecpD) polymerized tip adhesin of ECP fibers [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00022	42762	45287	+	yagX/ecpC	100.0	98.6	NP_286008	(yagX/ecpC) E. coli common pilus usher EcpC [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00022	42068	42736	+	yagY/ecpB	100.0	98.7	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00022	41423	42010	+	yagZ/ecpA	100.0	99.3	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00009	56661	57620	-	ybtA	100.0	99.5	NP_405473	(ybtA) transcriptional regulator YbtA [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00009	37306	38883	-	ybtE	100.0	99.8	NP_405468	(ybtE) yersiniabactin siderophore biosynthetic protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00009	57787	59589	+	ybtP	100.0	99.7	NP_405474	(ybtP) lipoprotein inner membrane ABC-transporter [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00009	59576	61378	+	ybtQ	100.0	99.7	NP_405475	(ybtQ) inner membrane ABC-transporter YbtQ [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00009	62679	63983	+	ybtS	100.0	99.6	NP_405477	(ybtS) salicylate synthase Irp9 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00009	38887	39690	-	ybtT	100.0	99.6	NP_405469	(ybtT) yersiniabactin biosynthetic protein YbtT [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00009	39687	40787	-	ybtU	100.0	99.5	NP_405470	(ybtU) yersiniabactin biosynthetic protein YbtU [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00009	61371	62651	+	ybtX	100.0	99.8	NP_405476	(ybtX) putative signal transducer [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00022	40758	41348	+	ykgK/ecpR	100.0	97.6	NP_286011	(ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

ID208

Contig	Start	End	Strand	Gene	Coverage	Identity	Accession	Product
contig00005	155908	156213	-	afaA	100.0	99.7	CAW30797	(afaA) fimbrial major subunit AfaA [Afimbrial adhesin AFA-I mannose-resistant adhesin (AI010)] [Escherichia coli O25b:H4 str. FV9863]
contig00005	154880	155624	-	afaB-I	100.0	99.9	CAW30798	(afaB-I) chaperone AfaB [Afimbrial adhesin AFA-I mannose-resistant adhesin (AI010)] [Escherichia coli O25b:H4 str. FV9863]
contig00005	152205	154787	-	afaC-I	100.0	99.7	CAW30799	(afaC-I) usher AfaC [Afimbrial adhesin AFA-I mannose-resistant adhesin (AI010)] [Escherichia coli O25b:H4 str. FV9863]
contig00005	150517	150999	-	afaE-V	100.0	97.3	CAA62863	(afaE-V) AfaE-V adhesin [Afimbrial adhesin AFA-V (AI013)] [Escherichia coli str. AL 851]
contig00016	67159	68587	+	aslA	100.0	97.4	AAG10151	(aslA) putative arylsulfatase [AslA (VF0238)] [Escherichia coli O18:K1:H7 str. RS218]
contig00003	73038	74066	-	chuS	100.0	98.0	NP_756169	(chuS) heme oxygenase ChuS [Chu (VF0227)] [Escherichia coli CFT073]
contig00003	76703	77695	+	chuT	100.0	99.4	NP_756175	(chuT) periplasmic heme-binding protein ChuT [Chu (VF0227)] [Escherichia coli CFT073]
contig00003	80231	81223	+	chuU	100.0	99.1	NP_756179	(chuU) heme permease protein ChuU [Chu (VF0227)] [Escherichia coli CFT073]
contig00003	81190	81990	+	chuV	100.0	98.4	NP_756180	(chuV) ATP-binding hydrophilic protein ChuV [Chu (VF0227)] [Escherichia coli CFT073]
contig00003	77715	79052	+	chuW	100.0	97.9	NP_756176	(chuW) Putative oxygen independent coproporphyrinogen III oxidase [Chu (VF0227)] [Escherichia coli CFT073]
contig00003	79559	80182	+	chuY	100.0	96.3	NP_756178	(chuY) ChuY [Chu (VF0227)] [Escherichia coli CFT073]
contig00022	84688	85143	-	csgB	99.8	83.8	NP_460114	(csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00052	68	718	+	csgD	100.0	81.3	NP_460113	(csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00052	1137	1553	+	csgF	99.0	81.2	NP_460111	(csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00052	1580	2413	+	csgG	100.0	82.8	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00005	159546	159773	+	daaF	100.0	100.0	AAA23662	(daaF) DaaF protein [F1845 fimbrial adhesin (AI016)] [Escherichia coli str. C1845]
contig00005	151746	152189	-	draD	100.0	99.8	AAK16478	(draD) DraD periplasmic protein [Dr adhesins (VF0223)] [Escherichia coli O75:K5:H- str. IH11128]
contig00005	151201	151374	-	draP	100.0	99.4	AAK16479	(draP) DraP [Dr adhesins (VF0223)] [Escherichia coli O75:K5:H- str. IH11128]
contig00046	25963	26709	-	entA	100.0	96.4	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00046	26709	27566	-	entB	100.0	98.2	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00046	29200	30387	-	entC	100.0	98.4	NP_752611	(entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00046	44844	45614	+	entD	100.0	93.9	NP_752599	(entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00046	27580	29190	-	entE	100.0	96.5	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00046	37063	40916	-	entF	99.3	96.3	NP_752604	(entF) enterobactin synthase multienzyme complex component ATP-dependent [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00046	31524	32774	-	entS	100.0	96.3	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00011	26968	28866	-	espL1	100.0	96.0	NP_288154	(espL1) Type III secretion system effector espL1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00092	8591	9841	+	espR1	99.3	94.7	NP_287686	(espR1) Type III secretion system effector espR1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00030	20282	21390	-	espR4	97.2	84.4	NP_288396	(espR4) Type III secretion system effector espR4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00006	5476	6896	-	espX1	99.9	95.2	NP_285716	(espX1) Type III secretion system effector EspX1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00006	45723	46471	+	espY1	99.5	94.4	NP_285753	(espY1) Type III secretion system effector EspY1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00006	62933	63502	+	espY2	100.0	94.0	NP_285765	(espY2) Type III secretion system effector EspY2 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00018	44736	47144	+	espY4	99.8	89.4	NP_290352	(espY4) Type III secretion system effector EspY4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00020	44563	48804	-	fdeC	99.8	92.0	YP_002390132	(fdeC) adhesin FdeC [FdeC (VF0506)] [Escherichia coli O45:K1:H7 str. S88]
contig00046	42579	44819	+	fepA	100.0	97.9	NP_752600	(fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00046	30564	31520	+	fepB	100.0	98.2	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00046	34875	35690	+	fepC	100.0	97.7	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00046	32873	33889	+	fepD	100.0	96.5	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00046	33886	34878	+	fepG	100.0	94.5	NP_752607	(fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00046	41134	42336	-	fes	100.0	97.0	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00025	62418	63022	-	fimA	99.8	90.8	NP_757241	(fimA) Type-1 fimbrial protein A chain precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00025	61052	61777	-	fimC	100.0	98.8	NP_757243	(fimC) Chaperone protein fimC precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00025	58349	60985	-	fimD	100.0	98.5	NP_757244	(fimD) Outer membrane usher protein fimD precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00025	63445	64041	-	fimE	100.0	98.8	NP_757240	(fimE) Type 1 fimbriae Regulatory protein fimE [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00025	57809	58342	-	fimF	100.0	96.6	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00025	57293	57796	-	fimG	100.0	98.2	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00025	56371	57282	-	fimH	100.0	97.5	NP_757248	(fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00025	61814	62353	-	fimI	100.0	98.5	NP_757242	(fimI) Fimbrin-like protein fimI precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00037	22990	25011	+	fyuA	100.0	99.8	NP_405467	(fyuA) pesticin/yersiniabactin receptor protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00343	897	1756	+	gspL	99.9	94.9	YP_404608	(gspL) general secretion pathway protein L [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00343	1872	2293	+	gspM	99.8	94.8	YP_404609	(gspM) general secretion pathway protein M [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00037	9890	19381	+	irp1	100.0	99.2	NP_405471	(irp1) yersiniabactin biosynthetic protein Irp1 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00037	3695	9802	+	irp2	100.0	99.8	NP_405472	(irp2) yersiniabactin biosynthetic protein Irp2 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00136	7017	8804	+	iucA	100.0	94.3	NP_755502	(iucA) aerobactin siderophore biosynthesis protein IucD [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00136	8805	9752	+	iucB	100.0	95.7	NP_755501	(iucB) aerobactin siderophore biosynthesis protein IucB [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00136	9752	11494	+	iucC	100.0	96.1	NP_755500	(iucC) aerobactin siderophore biosynthesis protein IucC [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00165	2678	4420	+	iucC	100.0	99.9	NP_709456	(iucC) aerobactin synthesis protein IucC [Aerobactin (VF0123)] [Shigella flexneri 2a str. 301]
contig00136	11491	12812	+	iucD	98.8	96.3	NP_755499	(iucD) L-lysine 6-monooxygenase IucD [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00165	4417	5754	+	iucD	100.0	99.8	NP_709457	(iucD) aerobactin synthesis protein IucC lysine 6-monooxygenase [Aerobactin (VF0123)] [Shigella flexneri 2a str. 301]
contig00136	12750	15051	+	iutA	100.0	88.4	NP_755498	(iutA) ferric aerobactin receptor precusor IutA [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00165	5676	7955	+	iutA	100.0	99.5	NP_755498	(iutA) ferric aerobactin receptor precusor IutA [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00134	7651	9327	-	kpsD	100.0	98.2	AAA21682	(kpsD) KpsD [K1 capsule (VF0239)] [Escherichia coli O18:K1:H7 str. RS218]
contig00343	3468	4244	+	kpsM	100.0	92.4	AAA24046	(kpsM) KpsM [K1 capsule (VF0239)] [Escherichia coli O18:K1:H7 str. RS218]
contig00009	103526	104566	-	ompA	100.0	98.1	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00097	9542	10587	-	ompA	99.0	84.7	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00195	1175	1488	-	papB	99.7	98.4		(papB) regulatory protein PapB [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig00426	96	635	+	papE	99.4	93.9	NP_755460	(papE) P pilus minor subunit PapE [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig00426	680	1213	+	papF	100.0	93.8	NP_755459	(papF) P pilus minor subunit PapF [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig00195	1893	2126	+	papI	100.0	95.3	NP_755468	(papI) regulatory protein PapI [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig00426	3734	4285	+	papX	100.0	97.6	NP_755457	(papX) PapX protein regulates flagellum synthesis to repress motility [P fimbriae (CVF425)] [Escherichia coli CFT073]
contig00165	8889	12788	+	sat	100.0	99.5	NP_755494	(sat) Aecreted auto transpoter toxin [Sat (VF0231)] [Escherichia coli CFT073]
contig00003	74115	76097	-	shuA	100.0	98.0	YP_405019	(shuA) outer membrane heme/hemoglobin receptor ShuA [Shu (VF0256)] [Shigella dysenteriae Sd197]
contig00003	79065	79559	+	shuX	100.0	96.6	YP_405016	(shuX) shu locus protein ShuX [Shu (VF0256)] [Shigella dysenteriae Sd197]
contig00020	64216	64969	+	yagV/ecpE	99.7	98.1	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00020	62649	64292	+	yagW/ecpD	100.0	99.1	NP_286007	(yagW/ecpD) polymerized tip adhesin of ECP fibers [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00020	60134	62659	+	yagX/ecpC	100.0	98.5	NP_286008	(yagX/ecpC) E. coli common pilus usher EcpC [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00020	59440	60108	+	yagY/ecpB	100.0	99.0	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00020	58795	59382	+	yagZ/ecpA	100.0	99.0	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00037	2545	3504	+	ybtA	100.0	99.5	NP_405473	(ybtA) transcriptional regulator YbtA [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00037	21282	22859	+	ybtE	100.0	99.8	NP_405468	(ybtE) yersiniabactin siderophore biosynthetic protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00037	576	2378	-	ybtP	100.0	99.7	NP_405474	(ybtP) lipoprotein inner membrane ABC-transporter [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00030	54432	55736	-	ybtS	100.0	99.7	NP_405477	(ybtS) salicylate synthase Irp9 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00037	20475	21278	+	ybtT	100.0	99.6	NP_405469	(ybtT) yersiniabactin biosynthetic protein YbtT [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00037	19378	20478	+	ybtU	100.0	99.7	NP_405470	(ybtU) yersiniabactin biosynthetic protein YbtU [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00030	55764	57044	-	ybtX	100.0	99.7	NP_405476	(ybtX) putative signal transducer [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00020	58130	58720	+	ykgK/ecpR	100.0	99.5	NP_286011	(ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

ID214

Contig	Start	End	Strand	Gene	Coverage	Identity	Accession	Product
contig00020	49276	50704	+	aslA	100.0	93.6	AAG10151	(aslA) putative arylsulfatase [AslA (VF0238)] [Escherichia coli O18:K1:H7 str. RS218]
contig00034	8086	8541	+	csgB	99.8	83.8	NP_460114	(csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00034	6681	7331	-	csgD	100.0	81.1	NP_460113	(csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00034	5846	6262	-	csgF	99.0	81.2	NP_460111	(csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00034	4986	5819	-	csgG	100.0	83.5	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00014	99075	99821	-	entA	100.0	95.7	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00014	99821	100678	-	entB	100.0	98.0	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00014	102312	103499	-	entC	100.0	97.8	NP_752611	(entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00014	118143	118913	+	entD	100.0	95.2	NP_752599	(entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00014	100692	102302	-	entE	100.0	95.5	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00014	110362	114215	-	entF	99.3	95.7	NP_752604	(entF) enterobactin synthase multienzyme complex component ATP-dependent [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00014	104822	106072	-	entS	100.0	95.4	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00012	6113	8012	-	espL1	100.0	97.5	NP_288154	(espL1) Type III secretion system effector espL1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00053	19363	21549	+	espL4	100.0	97.3	NP_290644	(espL4) Type III secretion system effector EspL4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00045	25904	26957	+	espR1	83.7	93.8	NP_287686	(espR1) Type III secretion system effector espR1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00003	203174	204595	+	espX1	100.0	95.2	NP_285716	(espX1) Type III secretion system effector EspX1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00043	8865	10445	+	espX4	99.9	93.3	NP_290672	(espX4) Type III secretion system effector EspX4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00003	164219	165030	-	espY1	99.9	87.0	NP_285753	(espY1) Type III secretion system effector EspY1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00005	19539	23787	+	fdeC	99.9	94.2	YP_002390132	(fdeC) adhesin FdeC [FdeC (VF0506)] [Escherichia coli O45:K1:H7 str. S88]
contig00014	115878	118118	+	fepA	100.0	96.7	NP_752600	(fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00014	103862	104818	+	fepB	100.0	97.5	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00014	108173	108988	+	fepC	100.0	97.3	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00014	106171	107187	+	fepD	100.0	96.1	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00014	107184	108176	+	fepG	100.0	94.1	NP_752607	(fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00014	114433	115635	-	fes	100.0	96.7	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00047	29974	30579	-	fimA	100.0	92.6	NP_757241	(fimA) Type-1 fimbrial protein A chain precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00047	32078	32680	-	fimB	100.0	98.2	NP_757239	(fimB) Type 1 fimbriae Regulatory protein fimB [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00047	28608	29333	-	fimC	100.0	98.5	NP_757243	(fimC) Chaperone protein fimC precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00047	25905	28541	-	fimD	100.0	98.2	NP_757244	(fimD) Outer membrane usher protein fimD precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00047	31004	31600	-	fimE	100.0	98.7	NP_757240	(fimE) Type 1 fimbriae Regulatory protein fimE [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00047	25365	25898	-	fimF	100.0	97.4	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00047	24849	25352	-	fimG	100.0	97.8	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00047	23927	24838	-	fimH	100.0	97.3	NP_757248	(fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00047	29370	29909	-	fimI	100.0	98.3	NP_757242	(fimI) Fimbrin-like protein fimI precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00017	63468	65489	+	fyuA	100.0	99.8	NP_405467	(fyuA) pesticin/yersiniabactin receptor protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00017	50381	59859	+	irp1	99.9	99.7	NP_405471	(irp1) yersiniabactin biosynthetic protein Irp1 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00017	44186	50293	+	irp2	100.0	99.8	NP_405472	(irp2) yersiniabactin biosynthetic protein Irp2 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00065	7017	8804	+	iucA	100.0	94.2	NP_755502	(iucA) aerobactin siderophore biosynthesis protein IucD [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00065	8805	9752	+	iucB	100.0	95.6	NP_755501	(iucB) aerobactin siderophore biosynthesis protein IucB [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00065	9752	11494	+	iucC	100.0	96.0	NP_755500	(iucC) aerobactin siderophore biosynthesis protein IucC [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00065	11491	12812	+	iucD	98.8	96.3	NP_755499	(iucD) L-lysine 6-monooxygenase IucD [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00065	12750	15051	+	iutA	100.0	88.4	NP_755498	(iutA) ferric aerobactin receptor precusor IutA [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00001	103766	104806	-	ompA	100.0	98.1	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00005	9679	10432	-	yagV/ecpE	99.7	97.1	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00005	10356	11999	-	yagW/ecpD	100.0	99.1	NP_286007	(yagW/ecpD) polymerized tip adhesin of ECP fibers [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00005	11989	14514	-	yagX/ecpC	100.0	98.7	NP_286008	(yagX/ecpC) E. coli common pilus usher EcpC [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00005	14540	15208	-	yagY/ecpB	100.0	98.1	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00005	15266	15853	-	yagZ/ecpA	100.0	99.2	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00017	43036	43995	+	ybtA	100.0	99.9	NP_405473	(ybtA) transcriptional regulator YbtA [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00017	61760	63337	+	ybtE	100.0	99.8	NP_405468	(ybtE) yersiniabactin siderophore biosynthetic protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00017	41067	42869	-	ybtP	100.0	99.7	NP_405474	(ybtP) lipoprotein inner membrane ABC-transporter [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00017	39278	41080	-	ybtQ	100.0	99.8	NP_405475	(ybtQ) inner membrane ABC-transporter YbtQ [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00017	36673	37977	-	ybtS	100.0	97.6	NP_405477	(ybtS) salicylate synthase Irp9 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00017	60953	61756	+	ybtT	100.0	99.9	NP_405469	(ybtT) yersiniabactin biosynthetic protein YbtT [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00017	59856	60956	+	ybtU	100.0	99.6	NP_405470	(ybtU) yersiniabactin biosynthetic protein YbtU [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00017	38005	39285	-	ybtX	100.0	97.7	NP_405476	(ybtX) putative signal transducer [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00005	15928	16518	-	ykgK/ecpR	100.0	97.0	NP_286011	(ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

ID224

Contig	Start	End	Strand	Gene	Coverage	Identity	Accession	Product
contig00020	49279	50707	+	aslA	100.0	93.6	AAG10151	(aslA) putative arylsulfatase [AslA (VF0238)] [Escherichia coli O18:K1:H7 str. RS218]
contig00018	6602	7057	+	csgB	99.8	83.8	NP_460114	(csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00018	5197	5847	-	csgD	100.0	81.1	NP_460113	(csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00018	4362	4778	-	csgF	99.0	81.2	NP_460111	(csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00018	3502	4335	-	csgG	100.0	83.5	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00013	99075	99821	-	entA	100.0	95.7	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00013	99821	100678	-	entB	100.0	98.1	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00013	102312	103499	-	entC	100.0	97.9	NP_752611	(entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00013	118143	118913	+	entD	100.0	95.2	NP_752599	(entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00013	100692	102302	-	entE	100.0	95.5	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00013	110362	114215	-	entF	99.3	95.7	NP_752604	(entF) enterobactin synthase multienzyme complex component ATP-dependent [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00013	104822	106072	-	entS	100.0	95.4	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00001	66086	67985	-	espL1	100.0	97.6	NP_288154	(espL1) Type III secretion system effector espL1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00036	37583	39769	+	espL4	100.0	97.3	NP_290644	(espL4) Type III secretion system effector EspL4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00043	25267	26320	+	espR1	83.7	93.8	NP_287686	(espR1) Type III secretion system effector espR1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00003	89032	90453	-	espX1	100.0	93.2	NP_285716	(espX1) Type III secretion system effector EspX1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00036	7787	9367	-	espX4	99.9	93.2	NP_290672	(espX4) Type III secretion system effector EspX4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00031	42346	43638	+	espX5	100.0	97.1	NP_290699	(espX5) Type III secretion system effector EspX5 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00003	128614	129425	+	espY1	99.9	87.0	NP_285753	(espY1) Type III secretion system effector EspY1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00047	21145	25393	-	fdeC	99.9	94.2	YP_002390132	(fdeC) adhesin FdeC [FdeC (VF0506)] [Escherichia coli O45:K1:H7 str. S88]
contig00013	115878	118118	+	fepA	100.0	96.7	NP_752600	(fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00013	103862	104818	+	fepB	100.0	97.5	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00013	108173	108988	+	fepC	100.0	97.3	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00013	106171	107187	+	fepD	100.0	96.1	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00013	107184	108176	+	fepG	100.0	94.1	NP_752607	(fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00013	114433	115635	-	fes	100.0	96.7	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00050	21382	21993	-	fimA	100.0	88.6	NP_757241	(fimA) Type-1 fimbrial protein A chain precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00050	23491	24093	-	fimB	100.0	98.2	NP_757239	(fimB) Type 1 fimbriae Regulatory protein fimB [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00050	20016	20741	-	fimC	100.0	98.9	NP_757243	(fimC) Chaperone protein fimC precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00050	17313	19949	-	fimD	100.0	98.6	NP_757244	(fimD) Outer membrane usher protein fimD precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00050	22420	23014	-	fimE	99.7	99.3	NP_757240	(fimE) Type 1 fimbriae Regulatory protein fimE [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00050	16773	17306	-	fimF	100.0	97.9	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00050	16257	16760	-	fimG	100.0	97.8	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00050	15335	16246	-	fimH	100.0	99.1	NP_757248	(fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00050	20778	21317	-	fimI	100.0	98.7	NP_757242	(fimI) Fimbrin-like protein fimI precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00005	30808	31638	+	gspC	100.0	94.7	YP_404599	(gspC) general secretion pathway protein C [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00005	31878	33728	+	gspD	100.0	96.1	YP_404600	(gspD) general secretion pathway protein D [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00005	33728	35221	+	gspE	100.0	96.9	YP_404601	(gspE) general secretion pathway protein E [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00005	35221	36420	+	gspF	100.0	96.0	YP_404602	(gspF) general secretion pathway protein F [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00005	36461	36916	+	gspG	100.0	95.0	YP_404603	(gspG) general secretion pathway protein G [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00005	36953	37482	+	gspH	99.8	94.9	YP_404604	(gspH) general secretion pathway protein H [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00005	37479	37850	+	gspI	100.0	95.2	YP_404605	(gspI) general secretion pathway protein I [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00005	37883	38452	+	gspJ	100.0	96.7	YP_404606	(gspJ) general secretion pathway protein J [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00005	38449	39426	+	gspK	100.0	97.0	YP_404607	(gspK) general secretion pathway protein K [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00005	39741	40601	+	gspL	100.0	97.0	YP_404608	(gspL) general secretion pathway protein L [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00005	40717	41139	+	gspM	100.0	98.3	YP_404609	(gspM) general secretion pathway protein M [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00004	103824	104864	-	ompA	100.0	98.1	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00059	5437	6190	+	yagV/ecpE	99.7	97.1	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00059	3870	5513	+	yagW/ecpD	100.0	99.1	NP_286007	(yagW/ecpD) polymerized tip adhesin of ECP fibers [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00059	1355	3880	+	yagX/ecpC	100.0	98.8	NP_286008	(yagX/ecpC) E. coli common pilus usher EcpC [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00059	661	1329	+	yagY/ecpB	100.0	98.1	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00059	16	603	+	yagZ/ecpA	100.0	99.2	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00047	28415	29005	+	ykgK/ecpR	100.0	97.0	NP_286011	(ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

ID228

Contig	Start	End	Strand	Gene	Coverage	Identity	Accession	Product
contig00019	73372	73677	-	afaA	100.0	100.0	CAW30797	(afaA) fimbrial major subunit AfaA [Afimbrial adhesin AFA-I mannose-resistant adhesin (AI010)] [Escherichia coli O25b:H4 str. FV9863]
contig00019	72344	73088	-	afaB-I	100.0	99.6	CAW30798	(afaB-I) chaperone AfaB [Afimbrial adhesin AFA-I mannose-resistant adhesin (AI010)] [Escherichia coli O25b:H4 str. FV9863]
contig00019	69669	72251	-	afaC-I	100.0	99.9	CAW30799	(afaC-I) usher AfaC [Afimbrial adhesin AFA-I mannose-resistant adhesin (AI010)] [Escherichia coli O25b:H4 str. FV9863]
contig00019	69210	69653	-	afaD	100.0	100.0	CAW30800	(afaD) AfaD [Afimbrial adhesin AFA-I mannose-resistant adhesin (AI010)] [Escherichia coli O25b:H4 str. FV9863]
contig00019	67972	68457	-	afaE-I	100.0	99.8	CAW30801	(afaE-I) AFA-I adhesin [Afa/Dr family (VF0212)] [Escherichia coli O25b:H4 str. FV9863]
contig00018	71089	72517	+	aslA	100.0	98.2	AAG10151	(aslA) putative arylsulfatase [AslA (VF0238)] [Escherichia coli O18:K1:H7 str. RS218]
contig00008	172126	174072	-	chuA	100.0	99.5	NP_756170	(chuA) Outer membrane heme/hemoglobin receptor ChuA [Chu (VF0227)] [Escherichia coli CFT073]
contig00008	171049	172077	-	chuS	100.0	99.0	NP_756169	(chuS) heme oxygenase ChuS [Chu (VF0227)] [Escherichia coli CFT073]
contig00008	174714	175706	+	chuT	100.0	99.8	NP_756175	(chuT) periplasmic heme-binding protein ChuT [Chu (VF0227)] [Escherichia coli CFT073]
contig00008	178242	179234	+	chuU	100.0	99.5	NP_756179	(chuU) heme permease protein ChuU [Chu (VF0227)] [Escherichia coli CFT073]
contig00008	179201	180001	+	chuV	100.0	99.8	NP_756180	(chuV) ATP-binding hydrophilic protein ChuV [Chu (VF0227)] [Escherichia coli CFT073]
contig00008	175726	177063	+	chuW	100.0	98.9	NP_756176	(chuW) Putative oxygen independent coproporphyrinogen III oxidase [Chu (VF0227)] [Escherichia coli CFT073]
contig00008	177076	177570	+	chuX	100.0	100.0	NP_756177	(chuX) putative heme-binding protein ChuX [Chu (VF0227)] [Escherichia coli CFT073]
contig00008	177570	178193	+	chuY	100.0	98.2	NP_756178	(chuY) ChuY [Chu (VF0227)] [Escherichia coli CFT073]
contig00011	102913	103368	-	csgB	99.8	83.8	NP_460114	(csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00011	104121	104771	+	csgD	100.0	81.6	NP_460113	(csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00011	105190	105606	+	csgF	99.0	80.8	NP_460111	(csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00011	105633	106466	+	csgG	100.0	83.2	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00019	74595	74822	+	daaF	100.0	100.0	AAA23662	(daaF) DaaF protein [F1845 fimbrial adhesin (AI016)] [Escherichia coli str. C1845]
contig00019	68659	68832	-	draP	100.0	98.8	AAK16479	(draP) DraP [Dr adhesins (VF0223)] [Escherichia coli O75:K5:H- str. IH11128]
contig00002	315696	316442	-	entA	100.0	98.1	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00002	316442	317299	-	entB	100.0	99.4	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00002	318933	320120	-	entC	100.0	98.7	NP_752611	(entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00002	334609	335270	+	entD	85.9	96.7	NP_752599	(entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00002	317313	318923	-	entE	100.0	98.9	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00002	326800	330681	-	entF	100.0	98.2	NP_752604	(entF) enterobactin synthase multienzyme complex component ATP-dependent [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00002	321257	322507	-	entS	100.0	97.4	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00003	228931	233178	-	fdeC	99.9	97.4	YP_002390132	(fdeC) adhesin FdeC [FdeC (VF0506)] [Escherichia coli O45:K1:H7 str. S88]
contig00002	332344	334584	+	fepA	100.0	98.9	NP_752600	(fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00002	320297	321253	+	fepB	100.0	98.4	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00002	324608	325423	+	fepC	100.0	99.1	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00002	322606	323622	+	fepD	100.0	97.8	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00002	323619	324611	+	fepG	100.0	97.9	NP_752607	(fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00002	330899	332101	-	fes	100.0	99.0	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00021	63524	64128	-	fimA	99.8	90.8	NP_757241	(fimA) Type-1 fimbrial protein A chain precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00021	62158	62883	-	fimC	100.0	98.9	NP_757243	(fimC) Chaperone protein fimC precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00021	59455	62091	-	fimD	100.0	98.5	NP_757244	(fimD) Outer membrane usher protein fimD precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00021	64551	65147	-	fimE	100.0	98.8	NP_757240	(fimE) Type 1 fimbriae Regulatory protein fimE [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00021	58915	59448	-	fimF	100.0	96.6	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00021	58399	58902	-	fimG	100.0	98.2	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00021	57477	58388	-	fimH	100.0	97.5	NP_757248	(fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00021	62920	63459	-	fimI	100.0	98.5	NP_757242	(fimI) Fimbrin-like protein fimI precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00026	24121	26142	-	fyuA	100.0	99.8	NP_405467	(fyuA) pesticin/yersiniabactin receptor protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00007	167409	168239	+	gspC	100.0	93.9	YP_404599	(gspC) general secretion pathway protein C [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00007	168479	170329	+	gspD	100.0	96.1	YP_404600	(gspD) general secretion pathway protein D [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00007	170329	171822	+	gspE	100.0	95.0	YP_404601	(gspE) general secretion pathway protein E [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00007	171822	173021	+	gspF	100.0	94.2	YP_404602	(gspF) general secretion pathway protein F [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00007	173062	173517	+	gspG	100.0	96.0	YP_404603	(gspG) general secretion pathway protein G [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00007	173554	174084	+	gspH	100.0	94.7	YP_404604	(gspH) general secretion pathway protein H [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00007	174081	174452	+	gspI	100.0	92.2	YP_404605	(gspI) general secretion pathway protein I [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00007	174485	175054	+	gspJ	100.0	94.4	YP_404606	(gspJ) general secretion pathway protein J [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00007	175051	176028	+	gspK	100.0	96.6	YP_404607	(gspK) general secretion pathway protein K [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00007	176343	177203	+	gspL	100.0	94.8	YP_404608	(gspL) general secretion pathway protein L [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00007	177319	177740	+	gspM	99.8	92.9	YP_404609	(gspM) general secretion pathway protein M [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00026	29751	39242	-	irp1	100.0	99.8	NP_405471	(irp1) yersiniabactin biosynthetic protein Irp1 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00026	39330	45437	-	irp2	100.0	99.4	NP_405472	(irp2) yersiniabactin biosynthetic protein Irp2 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00038	8835	10616	+	iucA	100.0	99.8	NP_709454	(iucA) aerobactin synthesis protein IucA [Aerobactin (VF0123)] [Shigella flexneri 2a str. 301]
contig00038	10617	11564	+	iucB	100.0	99.8	NP_709455	(iucB) aerobactin synthesis protein IucB [Aerobactin (VF0123)] [Shigella flexneri 2a str. 301]
contig00038	11564	13306	+	iucC	100.0	98.2	NP_755500	(iucC) aerobactin siderophore biosynthesis protein IucC [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00038	13303	14624	+	iucD	98.8	96.3	NP_755499	(iucD) L-lysine 6-monooxygenase IucD [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00038	14562	16863	+	iutA	100.0	88.4	NP_755498	(iutA) ferric aerobactin receptor precusor IutA [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00007	192461	194137	-	kpsD	100.0	98.3	AAA21682	(kpsD) KpsD [K1 capsule (VF0239)] [Escherichia coli O18:K1:H7 str. RS218]
contig00007	178799	179575	+	kpsM	100.0	94.7	AAA24046	(kpsM) KpsM [K1 capsule (VF0239)] [Escherichia coli O18:K1:H7 str. RS218]
contig00015	1055	2107	+	ompA	100.0	95.8	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00038	749	1062	-	papB	99.7	98.4		(papB) regulatory protein PapB [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig00038	1467	1700	+	papI	100.0	94.9	NP_755468	(papI) regulatory protein PapI [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig00092	763	1314	+	papX	100.0	97.6	NP_755457	(papX) PapX protein regulates flagellum synthesis to repress motility [P fimbriae (CVF425)] [Escherichia coli CFT073]
contig00038	17795	21694	+	sat	100.0	99.6	NP_755494	(sat) Aecreted auto transpoter toxin [Sat (VF0231)] [Escherichia coli CFT073]
contig00003	248516	249269	+	yagV/ecpE	99.7	98.0	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00003	246949	248592	+	yagW/ecpD	100.0	99.2	NP_286007	(yagW/ecpD) polymerized tip adhesin of ECP fibers [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00003	244434	246959	+	yagX/ecpC	100.0	97.6	NP_286008	(yagX/ecpC) E. coli common pilus usher EcpC [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00003	243740	244408	+	yagY/ecpB	100.0	98.1	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00003	243096	243683	+	yagZ/ecpA	100.0	98.5	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00026	45628	46587	-	ybtA	100.0	99.3	NP_405473	(ybtA) transcriptional regulator YbtA [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00026	26273	27850	-	ybtE	100.0	99.8	NP_405468	(ybtE) yersiniabactin siderophore biosynthetic protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00026	46754	48556	+	ybtP	100.0	99.6	NP_405474	(ybtP) lipoprotein inner membrane ABC-transporter [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00026	48543	50345	+	ybtQ	100.0	99.6	NP_405475	(ybtQ) inner membrane ABC-transporter YbtQ [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00026	51646	52950	+	ybtS	100.0	99.8	NP_405477	(ybtS) salicylate synthase Irp9 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00026	27854	28657	-	ybtT	100.0	99.6	NP_405469	(ybtT) yersiniabactin biosynthetic protein YbtT [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00026	28654	29754	-	ybtU	100.0	99.7	NP_405470	(ybtU) yersiniabactin biosynthetic protein YbtU [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00026	50338	51618	+	ybtX	100.0	99.7	NP_405476	(ybtX) putative signal transducer [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00003	242431	243021	+	ykgK/ecpR	100.0	99.5	NP_286011	(ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

ID229

Contig	Start	End	Strand	Gene	Coverage	Identity	Accession	Product
contig00001	473529	473984	-	csgB	99.8	84.0	NP_460114	(csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00001	474738	475388	+	csgD	100.0	81.1	NP_460113	(csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00001	475807	476223	+	csgF	99.0	81.2	NP_460111	(csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00001	476250	477083	+	csgG	100.0	83.1	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00012	99504	100250	-	entA	100.0	96.0	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00012	100250	101107	-	entB	100.0	97.9	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00012	102741	103928	-	entC	100.0	97.5	NP_752611	(entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00012	118572	119342	+	entD	100.0	94.0	NP_752599	(entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00012	101121	102731	-	entE	100.0	95.8	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00012	110815	114644	-	entF	98.7	95.4	NP_752604	(entF) enterobactin synthase multienzyme complex component ATP-dependent [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00012	105251	106501	-	entS	100.0	95.6	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00004	74456	76324	-	espL1	98.4	95.3	NP_288154	(espL1) Type III secretion system effector espL1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00030	24866	25921	+	espR1	83.8	94.2	NP_287686	(espR1) Type III secretion system effector espR1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00007	200479	201899	+	espX1	99.9	94.7	NP_285716	(espX1) Type III secretion system effector EspX1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00018	55542	57122	-	espX4	99.9	93.1	NP_290672	(espX4) Type III secretion system effector EspX4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00018	24730	26022	+	espX5	100.0	95.7	NP_290699	(espX5) Type III secretion system effector EspX5 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00016	43044	47285	-	fdeC	99.8	92.4	YP_002390132	(fdeC) adhesin FdeC [FdeC (VF0506)] [Escherichia coli O45:K1:H7 str. S88]
contig00012	116307	118547	+	fepA	100.0	96.8	NP_752600	(fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00012	104291	105247	+	fepB	100.0	97.4	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00012	108602	109417	+	fepC	100.0	97.3	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00012	106600	107616	+	fepD	100.0	96.0	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00012	107613	108605	+	fepG	100.0	94.0	NP_752607	(fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00012	114862	116064	-	fes	100.0	96.8	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00013	97591	98196	-	fimA	100.0	92.2	NP_757241	(fimA) Type-1 fimbrial protein A chain precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00013	99695	100297	-	fimB	100.0	98.2	NP_757239	(fimB) Type 1 fimbriae Regulatory protein fimB [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00013	96225	96950	-	fimC	100.0	98.5	NP_757243	(fimC) Chaperone protein fimC precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00013	93522	96158	-	fimD	100.0	98.3	NP_757244	(fimD) Outer membrane usher protein fimD precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00013	98621	99217	-	fimE	100.0	98.7	NP_757240	(fimE) Type 1 fimbriae Regulatory protein fimE [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00013	92982	93515	-	fimF	100.0	97.4	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00013	92466	92969	-	fimG	100.0	98.0	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00013	91544	92455	-	fimH	100.0	97.3	NP_757248	(fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00013	96987	97526	-	fimI	100.0	98.3	NP_757242	(fimI) Fimbrin-like protein fimI precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00002	353256	354086	-	gspC	100.0	95.1	YP_404599	(gspC) general secretion pathway protein C [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00002	351166	353016	-	gspD	100.0	97.0	YP_404600	(gspD) general secretion pathway protein D [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00002	349673	351166	-	gspE	100.0	97.1	YP_404601	(gspE) general secretion pathway protein E [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00002	348474	349673	-	gspF	100.0	96.2	YP_404602	(gspF) general secretion pathway protein F [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00002	347978	348433	-	gspG	100.0	95.6	YP_404603	(gspG) general secretion pathway protein G [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00002	347411	347941	-	gspH	100.0	96.0	YP_404604	(gspH) general secretion pathway protein H [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00002	347043	347414	-	gspI	100.0	95.2	YP_404605	(gspI) general secretion pathway protein I [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00002	346441	347010	-	gspJ	100.0	97.2	YP_404606	(gspJ) general secretion pathway protein J [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00002	345467	346444	-	gspK	100.0	96.1	YP_404607	(gspK) general secretion pathway protein K [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00002	344292	345152	-	gspL	100.0	97.6	YP_404608	(gspL) general secretion pathway protein L [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00002	343754	344176	-	gspM	100.0	94.1	YP_404609	(gspM) general secretion pathway protein M [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	546899	547951	+	ompA	100.0	94.3	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00016	56391	57144	+	yagV/ecpE	99.7	96.8	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00016	54824	56467	+	yagW/ecpD	100.0	98.6	NP_286007	(yagW/ecpD) polymerized tip adhesin of ECP fibers [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00016	52309	54834	+	yagX/ecpC	100.0	98.7	NP_286008	(yagX/ecpC) E. coli common pilus usher EcpC [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00016	51615	52283	+	yagY/ecpB	100.0	98.7	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00016	50970	51557	+	yagZ/ecpA	100.0	99.3	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00016	50305	50895	+	ykgK/ecpR	100.0	97.6	NP_286011	(ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

ID231

Contig	Start	End	Strand	Gene	Coverage	Identity	Accession	Product
contig00002	188648	189103	+	csgB	99.8	84.0	NP_460114	(csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00002	187244	187894	-	csgD	100.0	81.1	NP_460113	(csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00002	186409	186825	-	csgF	99.0	81.2	NP_460111	(csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00002	185549	186382	-	csgG	100.0	83.1	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00013	99546	100292	-	entA	100.0	96.0	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00013	100292	101149	-	entB	100.0	97.9	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00013	102783	103970	-	entC	100.0	97.5	NP_752611	(entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00013	118614	119384	+	entD	100.0	94.0	NP_752599	(entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00013	101163	102773	-	entE	100.0	95.8	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00013	110857	114686	-	entF	98.7	95.4	NP_752604	(entF) enterobactin synthase multienzyme complex component ATP-dependent [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00013	105293	106543	-	entS	100.0	95.6	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00008	74456	76324	-	espL1	98.4	95.3	NP_288154	(espL1) Type III secretion system effector espL1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00036	24866	25921	+	espR1	83.8	94.2	NP_287686	(espR1) Type III secretion system effector espR1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00011	142345	143765	+	espX1	99.9	94.7	NP_285716	(espX1) Type III secretion system effector EspX1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00019	55541	57121	-	espX4	99.9	93.1	NP_290672	(espX4) Type III secretion system effector EspX4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00019	24730	26022	+	espX5	100.0	95.7	NP_290699	(espX5) Type III secretion system effector EspX5 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00024	43044	47285	-	fdeC	99.8	92.4	YP_002390132	(fdeC) adhesin FdeC [FdeC (VF0506)] [Escherichia coli O45:K1:H7 str. S88]
contig00013	116349	118589	+	fepA	100.0	96.8	NP_752600	(fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00013	104333	105289	+	fepB	100.0	97.4	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00013	108644	109459	+	fepC	100.0	97.3	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00013	106642	107658	+	fepD	100.0	96.0	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00013	107655	108647	+	fepG	100.0	94.0	NP_752607	(fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00013	114904	116106	-	fes	100.0	96.8	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00016	107592	108196	-	fimA	99.8	90.6	NP_757241	(fimA) Type-1 fimbrial protein A chain precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00035	39364	39966	+	fimB	100.0	97.8	NP_757239	(fimB) Type 1 fimbriae Regulatory protein fimB [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00016	106220	106945	-	fimC	100.0	98.6	NP_757243	(fimC) Chaperone protein fimC precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00016	103517	106153	-	fimD	100.0	98.7	NP_757244	(fimD) Outer membrane usher protein fimD precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00035	40444	41040	+	fimE	100.0	99.2	NP_757240	(fimE) Type 1 fimbriae Regulatory protein fimE [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00016	102977	103510	-	fimF	100.0	96.6	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00016	102461	102964	-	fimG	100.0	97.8	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00016	101539	102450	-	fimH	100.0	97.7	NP_757248	(fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00016	106988	107527	-	fimI	100.0	99.1	NP_757242	(fimI) Fimbrin-like protein fimI precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00001	280819	281649	-	gspC	100.0	95.1	YP_404599	(gspC) general secretion pathway protein C [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	278729	280579	-	gspD	100.0	97.0	YP_404600	(gspD) general secretion pathway protein D [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	277236	278729	-	gspE	100.0	97.1	YP_404601	(gspE) general secretion pathway protein E [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	276037	277236	-	gspF	100.0	96.2	YP_404602	(gspF) general secretion pathway protein F [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	275541	275996	-	gspG	100.0	95.6	YP_404603	(gspG) general secretion pathway protein G [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	274974	275504	-	gspH	100.0	96.0	YP_404604	(gspH) general secretion pathway protein H [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	274606	274977	-	gspI	100.0	95.2	YP_404605	(gspI) general secretion pathway protein I [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	274004	274573	-	gspJ	100.0	97.2	YP_404606	(gspJ) general secretion pathway protein J [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	273030	274007	-	gspK	100.0	96.1	YP_404607	(gspK) general secretion pathway protein K [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	271855	272715	-	gspL	100.0	97.6	YP_404608	(gspL) general secretion pathway protein L [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	271317	271739	-	gspM	100.0	94.1	YP_404609	(gspM) general secretion pathway protein M [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00002	114681	115733	-	ompA	100.0	94.3	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00024	56391	57144	+	yagV/ecpE	99.7	96.8	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00024	54824	56467	+	yagW/ecpD	100.0	98.5	NP_286007	(yagW/ecpD) polymerized tip adhesin of ECP fibers [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00024	52309	54834	+	yagX/ecpC	100.0	98.7	NP_286008	(yagX/ecpC) E. coli common pilus usher EcpC [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00024	51615	52283	+	yagY/ecpB	100.0	98.7	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00024	50970	51557	+	yagZ/ecpA	100.0	99.3	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00024	50305	50895	+	ykgK/ecpR	100.0	97.6	NP_286011	(ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

ID233

Contig	Start	End	Strand	Gene	Coverage	Identity	Accession	Product
contig00049	9390	9504	+	astA	98.3	88.7	BAA94855	(astA) heat-stable enterotoxin 1 [EAST1 (VF0216)] [Escherichia coli O44:H18 042]
contig00693	123	894	+	fepC	94.6	80.8	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00070	10289	11341	-	ompA	100.0	85.2	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00499	320	1073	-	yagV/ecpE	99.7	85.4	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00499	999	2534	-	yagW/ecpD	93.4	89.7	NP_286007	(yagW/ecpD) polymerized tip adhesin of ECP fibers [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00171	6061	8586	+	yagX/ecpC	100.0	87.5	NP_286008	(yagX/ecpC) E. coli common pilus usher EcpC [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00171	5367	6035	+	yagY/ecpB	100.0	86.2	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00171	4722	5305	+	yagZ/ecpA	99.3	89.6	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00171	4067	4647	+	ykgK/ecpR	98.3	87.4	NP_286011	(ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

ID235

Contig	Start	End	Strand	Gene	Coverage	Identity	Accession	Product
contig00040	18172	18477	-	afaA	100.0	100.0	CAW30797	(afaA) fimbrial major subunit AfaA [Afimbrial adhesin AFA-I mannose-resistant adhesin (AI010)] [Escherichia coli O25b:H4 str. FV9863]
contig00040	17123	17867	-	afaB-I	100.0	99.7	CAW30798	(afaB-I) chaperone AfaB [Afimbrial adhesin AFA-I mannose-resistant adhesin (AI010)] [Escherichia coli O25b:H4 str. FV9863]
contig00040	14448	17030	-	afaC-I	100.0	99.8	CAW30799	(afaC-I) usher AfaC [Afimbrial adhesin AFA-I mannose-resistant adhesin (AI010)] [Escherichia coli O25b:H4 str. FV9863]
contig00040	12760	13242	-	afaE-V	100.0	83.8	CAA62863	(afaE-V) AfaE-V adhesin [Afimbrial adhesin AFA-V (AI013)] [Escherichia coli str. AL 851]
contig00017	67243	68671	+	aslA	100.0	97.4	AAG10151	(aslA) putative arylsulfatase [AslA (VF0238)] [Escherichia coli O18:K1:H7 str. RS218]
contig00009	73038	74066	-	chuS	100.0	98.0	NP_756169	(chuS) heme oxygenase ChuS [Chu (VF0227)] [Escherichia coli CFT073]
contig00009	76703	77695	+	chuT	100.0	99.4	NP_756175	(chuT) periplasmic heme-binding protein ChuT [Chu (VF0227)] [Escherichia coli CFT073]
contig00009	80231	81223	+	chuU	100.0	99.1	NP_756179	(chuU) heme permease protein ChuU [Chu (VF0227)] [Escherichia coli CFT073]
contig00009	81190	81990	+	chuV	100.0	98.4	NP_756180	(chuV) ATP-binding hydrophilic protein ChuV [Chu (VF0227)] [Escherichia coli CFT073]
contig00009	77715	79052	+	chuW	100.0	97.9	NP_756176	(chuW) Putative oxygen independent coproporphyrinogen III oxidase [Chu (VF0227)] [Escherichia coli CFT073]
contig00009	79559	80182	+	chuY	100.0	96.3	NP_756178	(chuY) ChuY [Chu (VF0227)] [Escherichia coli CFT073]
contig00012	163196	163651	-	csgB	99.8	83.8	NP_460114	(csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00011	174374	175024	-	csgD	100.0	81.3	NP_460113	(csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00011	173539	173955	-	csgF	99.0	81.2	NP_460111	(csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00011	172679	173512	-	csgG	100.0	82.8	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00040	19395	19622	+	daaF	100.0	100.0	AAA23662	(daaF) DaaF protein [F1845 fimbrial adhesin (AI016)] [Escherichia coli str. C1845]
contig00040	13989	14432	-	draD	100.0	99.8	AAK16478	(draD) DraD periplasmic protein [Dr adhesins (VF0223)] [Escherichia coli O75:K5:H- str. IH11128]
contig00040	13444	13617	-	draP	100.0	98.8	AAK16479	(draP) DraP [Dr adhesins (VF0223)] [Escherichia coli O75:K5:H- str. IH11128]
contig00003	337366	338112	-	entA	100.0	96.4	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00003	338112	338969	-	entB	100.0	98.2	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00003	340603	341790	-	entC	100.0	98.4	NP_752611	(entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00003	356247	357017	+	entD	100.0	93.9	NP_752599	(entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00003	338983	340593	-	entE	100.0	96.5	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00003	348466	352319	-	entF	99.3	96.3	NP_752604	(entF) enterobactin synthase multienzyme complex component ATP-dependent [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00003	342927	344177	-	entS	100.0	96.3	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00002	198794	200692	-	espL1	100.0	96.0	NP_288154	(espL1) Type III secretion system effector espL1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00025	49102	50352	+	espR1	99.3	94.7	NP_287686	(espR1) Type III secretion system effector espR1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00022	20282	21390	-	espR4	97.2	84.4	NP_288396	(espR4) Type III secretion system effector espR4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00007	5476	6896	-	espX1	99.9	95.2	NP_285716	(espX1) Type III secretion system effector EspX1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00021	57193	58773	+	espX4	100.0	96.0	NP_290672	(espX4) Type III secretion system effector EspX4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00007	45723	46471	+	espY1	99.5	94.4	NP_285753	(espY1) Type III secretion system effector EspY1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00007	62933	63502	+	espY2	100.0	94.0	NP_285765	(espY2) Type III secretion system effector EspY2 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00020	44513	48754	-	fdeC	99.8	92.0	YP_002390132	(fdeC) adhesin FdeC [FdeC (VF0506)] [Escherichia coli O45:K1:H7 str. S88]
contig00003	353982	356222	+	fepA	100.0	97.9	NP_752600	(fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00003	341967	342923	+	fepB	100.0	98.2	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00003	346278	347093	+	fepC	100.0	97.7	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00003	344276	345292	+	fepD	100.0	96.5	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00003	345289	346281	+	fepG	100.0	94.5	NP_752607	(fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00003	352537	353739	-	fes	100.0	97.0	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00034	7887	9908	+	fyuA	100.0	99.8	NP_405467	(fyuA) pesticin/yersiniabactin receptor protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00005	32245	33075	-	gspC	100.0	93.9	YP_404599	(gspC) general secretion pathway protein C [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00005	30155	32005	-	gspD	100.0	96.0	YP_404600	(gspD) general secretion pathway protein D [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00005	28662	30155	-	gspE	100.0	95.3	YP_404601	(gspE) general secretion pathway protein E [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00005	27463	28662	-	gspF	100.0	95.4	YP_404602	(gspF) general secretion pathway protein F [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00005	26967	27422	-	gspG	100.0	95.8	YP_404603	(gspG) general secretion pathway protein G [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00005	26400	26930	-	gspH	100.0	95.5	YP_404604	(gspH) general secretion pathway protein H [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00005	26032	26403	-	gspI	100.0	94.4	YP_404605	(gspI) general secretion pathway protein I [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00005	25430	25999	-	gspJ	100.0	96.0	YP_404606	(gspJ) general secretion pathway protein J [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00005	24456	25433	-	gspK	100.0	96.7	YP_404607	(gspK) general secretion pathway protein K [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00005	23281	24141	-	gspL	100.0	94.7	YP_404608	(gspL) general secretion pathway protein L [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00005	22744	23165	-	gspM	99.8	91.9	YP_404609	(gspM) general secretion pathway protein M [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00022	61945	68052	+	irp2	100.0	99.8	NP_405472	(irp2) yersiniabactin biosynthetic protein Irp2 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00055	1586	3373	-	iucA	100.0	94.3	NP_755502	(iucA) aerobactin siderophore biosynthesis protein IucD [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00059	2017	3798	+	iucA	100.0	99.8	NP_709454	(iucA) aerobactin synthesis protein IucA [Aerobactin (VF0123)] [Shigella flexneri 2a str. 301]
contig00055	638	1585	-	iucB	100.0	95.7	NP_755501	(iucB) aerobactin siderophore biosynthesis protein IucB [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00059	3799	4746	+	iucB	100.0	99.8	NP_709455	(iucB) aerobactin synthesis protein IucB [Aerobactin (VF0123)] [Shigella flexneri 2a str. 301]
contig00059	4746	6488	+	iucC	100.0	98.0	NP_755500	(iucC) aerobactin siderophore biosynthesis protein IucC [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00059	6485	7806	+	iucD	98.8	96.3	NP_755499	(iucD) L-lysine 6-monooxygenase IucD [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00005	9975	11651	+	kpsD	100.0	98.3	AAA21682	(kpsD) KpsD [K1 capsule (VF0239)] [Escherichia coli O18:K1:H7 str. RS218]
contig00005	20905	21681	-	kpsM	100.0	94.5	AAA24046	(kpsM) KpsM [K1 capsule (VF0239)] [Escherichia coli O18:K1:H7 str. RS218]
contig00011	103614	104654	-	ompA	100.0	98.1	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00060	749	1062	-	papB	99.7	98.4		(papB) regulatory protein PapB [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig00060	1467	1700	+	papI	100.0	94.9	NP_755468	(papI) regulatory protein PapI [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig00087	256	807	+	papX	100.0	97.6	NP_755457	(papX) PapX protein regulates flagellum synthesis to repress motility [P fimbriae (CVF425)] [Escherichia coli CFT073]
contig00069	941	4840	+	sat	100.0	99.6	NP_755494	(sat) Aecreted auto transpoter toxin [Sat (VF0231)] [Escherichia coli CFT073]
contig00009	74115	76097	-	shuA	100.0	98.0	YP_405019	(shuA) outer membrane heme/hemoglobin receptor ShuA [Shu (VF0256)] [Shigella dysenteriae Sd197]
contig00009	79065	79559	+	shuX	100.0	96.6	YP_405016	(shuX) shu locus protein ShuX [Shu (VF0256)] [Shigella dysenteriae Sd197]
contig00020	64166	64919	+	yagV/ecpE	99.7	98.1	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00020	62599	64242	+	yagW/ecpD	100.0	99.1	NP_286007	(yagW/ecpD) polymerized tip adhesin of ECP fibers [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00020	60084	62609	+	yagX/ecpC	100.0	98.5	NP_286008	(yagX/ecpC) E. coli common pilus usher EcpC [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00020	59390	60058	+	yagY/ecpB	100.0	99.0	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00020	58745	59332	+	yagZ/ecpA	100.0	99.0	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00022	60795	61754	+	ybtA	100.0	99.5	NP_405473	(ybtA) transcriptional regulator YbtA [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00034	6179	7756	+	ybtE	100.0	99.9	NP_405468	(ybtE) yersiniabactin siderophore biosynthetic protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00022	58826	60628	-	ybtP	100.0	99.7	NP_405474	(ybtP) lipoprotein inner membrane ABC-transporter [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00022	57037	58839	-	ybtQ	100.0	99.7	NP_405475	(ybtQ) inner membrane ABC-transporter YbtQ [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00022	54432	55736	-	ybtS	100.0	99.7	NP_405477	(ybtS) salicylate synthase Irp9 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00034	5372	6175	+	ybtT	100.0	99.6	NP_405469	(ybtT) yersiniabactin biosynthetic protein YbtT [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00034	4275	5375	+	ybtU	100.0	99.7	NP_405470	(ybtU) yersiniabactin biosynthetic protein YbtU [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00022	55764	57044	-	ybtX	100.0	99.7	NP_405476	(ybtX) putative signal transducer [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00020	58080	58670	+	ykgK/ecpR	100.0	99.7	NP_286011	(ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

ID237

Contig	Start	End	Strand	Gene	Coverage	Identity	Accession	Product
contig00001	446599	447054	-	csgB	99.8	84.0	NP_460114	(csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00001	447808	448458	+	csgD	100.0	81.1	NP_460113	(csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00001	448877	449293	+	csgF	99.0	81.2	NP_460111	(csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00001	449320	450153	+	csgG	100.0	83.1	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00009	99596	100342	-	entA	100.0	96.0	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00009	100342	101199	-	entB	100.0	97.9	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00009	102833	104020	-	entC	100.0	97.5	NP_752611	(entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00009	118664	119434	+	entD	100.0	94.0	NP_752599	(entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00009	101213	102823	-	entE	100.0	95.8	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00009	110907	114736	-	entF	98.7	95.4	NP_752604	(entF) enterobactin synthase multienzyme complex component ATP-dependent [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00009	105343	106593	-	entS	100.0	95.6	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00011	74456	76324	-	espL1	98.4	95.3	NP_288154	(espL1) Type III secretion system effector espL1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00033	24866	25921	+	espR1	83.8	94.2	NP_287686	(espR1) Type III secretion system effector espR1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00013	142372	143792	+	espX1	99.9	94.7	NP_285716	(espX1) Type III secretion system effector EspX1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00014	39590	41170	+	espX4	99.9	93.1	NP_290672	(espX4) Type III secretion system effector EspX4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00014	70690	71982	-	espX5	100.0	95.7	NP_290699	(espX5) Type III secretion system effector EspX5 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00018	43044	47285	-	fdeC	99.8	92.4	YP_002390132	(fdeC) adhesin FdeC [FdeC (VF0506)] [Escherichia coli O45:K1:H7 str. S88]
contig00009	116399	118639	+	fepA	100.0	96.8	NP_752600	(fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00009	104383	105339	+	fepB	100.0	97.4	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00009	108694	109509	+	fepC	100.0	97.3	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00009	106692	107708	+	fepD	100.0	96.0	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00009	107705	108697	+	fepG	100.0	94.0	NP_752607	(fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00009	114954	116156	-	fes	100.0	96.8	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00019	97591	98196	-	fimA	100.0	92.2	NP_757241	(fimA) Type-1 fimbrial protein A chain precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00038	27228	27830	+	fimB	100.0	98.2	NP_757239	(fimB) Type 1 fimbriae Regulatory protein fimB [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00019	96225	96950	-	fimC	100.0	98.5	NP_757243	(fimC) Chaperone protein fimC precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00019	93522	96158	-	fimD	100.0	98.3	NP_757244	(fimD) Outer membrane usher protein fimD precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00038	28308	28904	+	fimE	100.0	98.7	NP_757240	(fimE) Type 1 fimbriae Regulatory protein fimE [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00019	92982	93515	-	fimF	100.0	97.4	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00019	92466	92969	-	fimG	100.0	98.0	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00019	91544	92455	-	fimH	100.0	97.3	NP_757248	(fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00019	96987	97526	-	fimI	100.0	98.3	NP_757242	(fimI) Fimbrin-like protein fimI precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00002	353256	354086	-	gspC	100.0	95.1	YP_404599	(gspC) general secretion pathway protein C [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00002	351166	353016	-	gspD	100.0	97.0	YP_404600	(gspD) general secretion pathway protein D [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00002	349673	351166	-	gspE	100.0	97.1	YP_404601	(gspE) general secretion pathway protein E [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00002	348474	349673	-	gspF	100.0	96.2	YP_404602	(gspF) general secretion pathway protein F [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00002	347978	348433	-	gspG	100.0	95.6	YP_404603	(gspG) general secretion pathway protein G [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00002	347411	347941	-	gspH	100.0	96.0	YP_404604	(gspH) general secretion pathway protein H [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00002	347043	347414	-	gspI	100.0	95.2	YP_404605	(gspI) general secretion pathway protein I [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00002	346441	347010	-	gspJ	100.0	97.2	YP_404606	(gspJ) general secretion pathway protein J [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00002	345467	346444	-	gspK	100.0	96.1	YP_404607	(gspK) general secretion pathway protein K [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00002	344292	345152	-	gspL	100.0	97.6	YP_404608	(gspL) general secretion pathway protein L [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00002	343754	344176	-	gspM	100.0	94.1	YP_404609	(gspM) general secretion pathway protein M [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00010	104187	105239	-	ompA	100.0	94.3	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00018	56391	57144	+	yagV/ecpE	99.7	96.8	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00018	54824	56467	+	yagW/ecpD	100.0	98.6	NP_286007	(yagW/ecpD) polymerized tip adhesin of ECP fibers [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00018	52309	54834	+	yagX/ecpC	100.0	98.6	NP_286008	(yagX/ecpC) E. coli common pilus usher EcpC [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00018	51615	52283	+	yagY/ecpB	100.0	98.7	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00018	50970	51557	+	yagZ/ecpA	100.0	99.3	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00018	50305	50895	+	ykgK/ecpR	100.0	97.6	NP_286011	(ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

ID256

Contig	Start	End	Strand	Gene	Coverage	Identity	Accession	Product
contig00053	6790	7534	-	afaB-I	100.0	98.2	CAW30798	(afaB-I) chaperone AfaB [Afimbrial adhesin AFA-I mannose-resistant adhesin (AI010)] [Escherichia coli O25b:H4 str. FV9863]
contig00053	4115	6697	-	afaC-I	100.0	99.0	CAW30799	(afaC-I) usher AfaC [Afimbrial adhesin AFA-I mannose-resistant adhesin (AI010)] [Escherichia coli O25b:H4 str. FV9863]
contig00015	71396	72824	+	aslA	100.0	98.2	AAG10151	(aslA) putative arylsulfatase [AslA (VF0238)] [Escherichia coli O18:K1:H7 str. RS218]
contig00004	114245	116191	-	chuA	100.0	99.5	NP_756170	(chuA) Outer membrane heme/hemoglobin receptor ChuA [Chu (VF0227)] [Escherichia coli CFT073]
contig00004	113168	114196	-	chuS	100.0	99.0	NP_756169	(chuS) heme oxygenase ChuS [Chu (VF0227)] [Escherichia coli CFT073]
contig00004	116834	117826	+	chuT	100.0	99.8	NP_756175	(chuT) periplasmic heme-binding protein ChuT [Chu (VF0227)] [Escherichia coli CFT073]
contig00004	120362	121354	+	chuU	100.0	99.3	NP_756179	(chuU) heme permease protein ChuU [Chu (VF0227)] [Escherichia coli CFT073]
contig00004	121321	122121	+	chuV	100.0	99.8	NP_756180	(chuV) ATP-binding hydrophilic protein ChuV [Chu (VF0227)] [Escherichia coli CFT073]
contig00004	117846	119183	+	chuW	100.0	99.2	NP_756176	(chuW) Putative oxygen independent coproporphyrinogen III oxidase [Chu (VF0227)] [Escherichia coli CFT073]
contig00004	119196	119690	+	chuX	100.0	100.0	NP_756177	(chuX) putative heme-binding protein ChuX [Chu (VF0227)] [Escherichia coli CFT073]
contig00004	119690	120313	+	chuY	100.0	98.4	NP_756178	(chuY) ChuY [Chu (VF0227)] [Escherichia coli CFT073]
contig00010	164930	165385	+	csgB	99.8	83.8	NP_460114	(csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00010	163527	164177	-	csgD	100.0	81.6	NP_460113	(csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00010	162692	163108	-	csgF	99.0	80.8	NP_460111	(csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00010	161832	162665	-	csgG	100.0	83.2	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00053	8925	9152	+	daaF	100.0	100.0	AAA23662	(daaF) DaaF protein [F1845 fimbrial adhesin (AI016)] [Escherichia coli str. C1845]
contig00053	7816	8121	-	draA	100.0	100.0	AAK16475	(draA) cytoplamic protein DraA [Dr adhesins (VF0223)] [Escherichia coli O75:K5:H- str. IH11128]
contig00053	3656	4099	-	draD	100.0	99.8	AAK16478	(draD) DraD periplasmic protein [Dr adhesins (VF0223)] [Escherichia coli O75:K5:H- str. IH11128]
contig00053	2358	2917	-	draE2	99.6	99.6	AAB65153	(draE2) Dr-II structural adhesin precursor [Afa/Dr family (VF0212)] [Escherichia coli EC7372]
contig00053	3104	3277	-	draP	100.0	99.4	AAK16479	(draP) DraP [Dr adhesins (VF0223)] [Escherichia coli O75:K5:H- str. IH11128]
contig00001	315687	316433	-	entA	100.0	98.1	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00001	316433	317290	-	entB	100.0	99.5	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00001	318924	320111	-	entC	100.0	99.4	NP_752611	(entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00001	334569	335230	+	entD	85.9	97.7	NP_752599	(entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00001	317304	318914	-	entE	100.0	99.1	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00001	326788	330641	-	entF	99.3	97.8	NP_752604	(entF) enterobactin synthase multienzyme complex component ATP-dependent [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00001	321248	322498	-	entS	100.0	98.2	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00022	11557	15804	-	fdeC	99.9	97.4	YP_002390132	(fdeC) adhesin FdeC [FdeC (VF0506)] [Escherichia coli O45:K1:H7 str. S88]
contig00001	332304	334544	+	fepA	100.0	98.8	NP_752600	(fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00001	320288	321244	+	fepB	100.0	99.7	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00001	324599	325414	+	fepC	100.0	99.1	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00001	322597	323613	+	fepD	100.0	97.8	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00001	323610	324602	+	fepG	100.0	97.7	NP_752607	(fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00001	330859	332061	-	fes	100.0	99.2	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00039	12072	12676	-	fimA	99.8	90.8	NP_757241	(fimA) Type-1 fimbrial protein A chain precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00039	14174	14776	-	fimB	100.0	97.8	NP_757239	(fimB) Type 1 fimbriae Regulatory protein fimB [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00039	10706	11431	-	fimC	100.0	98.6	NP_757243	(fimC) Chaperone protein fimC precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00039	8003	10639	-	fimD	100.0	98.9	NP_757244	(fimD) Outer membrane usher protein fimD precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00039	13100	13696	-	fimE	100.0	98.8	NP_757240	(fimE) Type 1 fimbriae Regulatory protein fimE [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00039	7463	7996	-	fimF	100.0	99.1	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00039	6947	7450	-	fimG	100.0	98.2	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00039	6025	6936	-	fimH	100.0	97.6	NP_757248	(fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00039	11468	12007	-	fimI	100.0	98.5	NP_757242	(fimI) Fimbrin-like protein fimI precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00021	76644	78665	+	fyuA	100.0	99.9	NP_405467	(fyuA) pesticin/yersiniabactin receptor protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00003	27806	28636	-	gspC	100.0	94.6	YP_404599	(gspC) general secretion pathway protein C [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00003	25716	27566	-	gspD	100.0	96.1	YP_404600	(gspD) general secretion pathway protein D [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00003	24223	25716	-	gspE	100.0	94.8	YP_404601	(gspE) general secretion pathway protein E [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00003	23024	24223	-	gspF	100.0	94.2	YP_404602	(gspF) general secretion pathway protein F [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00003	22528	22983	-	gspG	100.0	95.8	YP_404603	(gspG) general secretion pathway protein G [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00003	21961	22491	-	gspH	100.0	96.6	YP_404604	(gspH) general secretion pathway protein H [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00003	21593	21964	-	gspI	100.0	94.6	YP_404605	(gspI) general secretion pathway protein I [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00003	20991	21560	-	gspJ	100.0	94.4	YP_404606	(gspJ) general secretion pathway protein J [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00003	20017	20994	-	gspK	100.0	94.5	YP_404607	(gspK) general secretion pathway protein K [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00003	18842	19702	-	gspL	100.0	93.3	YP_404608	(gspL) general secretion pathway protein L [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00003	18317	18726	-	gspM	96.9	93.4	YP_404609	(gspM) general secretion pathway protein M [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00021	63543	73034	+	irp1	100.0	99.7	NP_405471	(irp1) yersiniabactin biosynthetic protein Irp1 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00021	57348	63455	+	irp2	100.0	99.5	NP_405472	(irp2) yersiniabactin biosynthetic protein Irp2 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00044	2017	3798	+	iucA	100.0	99.8	NP_709454	(iucA) aerobactin synthesis protein IucA [Aerobactin (VF0123)] [Shigella flexneri 2a str. 301]
contig00044	3799	4746	+	iucB	100.0	99.8	NP_709455	(iucB) aerobactin synthesis protein IucB [Aerobactin (VF0123)] [Shigella flexneri 2a str. 301]
contig00044	4746	6488	+	iucC	100.0	98.1	NP_755500	(iucC) aerobactin siderophore biosynthesis protein IucC [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00044	6485	7806	+	iucD	98.8	96.3	NP_755499	(iucD) L-lysine 6-monooxygenase IucD [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00044	7744	10045	+	iutA	100.0	88.4	NP_755498	(iutA) ferric aerobactin receptor precusor IutA [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00003	3663	5339	+	kpsD	100.0	99.5	AAA21682	(kpsD) KpsD [K1 capsule (VF0239)] [Escherichia coli O18:K1:H7 str. RS218]
contig00003	16383	17159	-	kpsM	100.0	91.1	AAA24046	(kpsM) KpsM [K1 capsule (VF0239)] [Escherichia coli O18:K1:H7 str. RS218]
contig00010	93898	94950	-	ompA	100.0	95.8	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00062	2776	3089	-	papB	99.7	98.4		(papB) regulatory protein PapB [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig00062	3495	3728	+	papI	100.0	94.9	NP_755468	(papI) regulatory protein PapI [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig00062	451	1002	-	papX	100.0	97.6	NP_755457	(papX) PapX protein regulates flagellum synthesis to repress motility [P fimbriae (CVF425)] [Escherichia coli CFT073]
contig00044	10977	14876	+	sat	100.0	99.5	NP_755494	(sat) Aecreted auto transpoter toxin [Sat (VF0231)] [Escherichia coli CFT073]
contig00054	8438	9576	+	senB	99.9	99.7	YP_406304	(senB) enterotoxin [ShET2 (VF0258)] [Shigella flexneri 2a str. 301]
contig00022	31142	31895	+	yagV/ecpE	99.7	98.0	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00022	29575	31218	+	yagW/ecpD	100.0	99.1	NP_286007	(yagW/ecpD) polymerized tip adhesin of ECP fibers [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00022	27060	29585	+	yagX/ecpC	100.0	97.6	NP_286008	(yagX/ecpC) E. coli common pilus usher EcpC [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00022	26366	27034	+	yagY/ecpB	100.0	98.1	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00022	25722	26309	+	yagZ/ecpA	100.0	98.3	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00021	56198	57157	+	ybtA	100.0	99.5	NP_405473	(ybtA) transcriptional regulator YbtA [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00021	74935	76512	+	ybtE	100.0	99.8	NP_405468	(ybtE) yersiniabactin siderophore biosynthetic protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00021	54229	56031	-	ybtP	100.0	99.6	NP_405474	(ybtP) lipoprotein inner membrane ABC-transporter [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00021	52440	54242	-	ybtQ	100.0	99.6	NP_405475	(ybtQ) inner membrane ABC-transporter YbtQ [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00021	49835	51139	-	ybtS	100.0	99.8	NP_405477	(ybtS) salicylate synthase Irp9 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00021	74128	74931	+	ybtT	100.0	99.5	NP_405469	(ybtT) yersiniabactin biosynthetic protein YbtT [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00021	73031	74131	+	ybtU	100.0	99.6	NP_405470	(ybtU) yersiniabactin biosynthetic protein YbtU [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00021	51167	52447	-	ybtX	100.0	99.5	NP_405476	(ybtX) putative signal transducer [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00022	25057	25647	+	ykgK/ecpR	100.0	99.5	NP_286011	(ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

ID263

Contig	Start	End	Strand	Gene	Coverage	Identity	Accession	Product
contig00020	49279	50707	+	aslA	100.0	93.6	AAG10151	(aslA) putative arylsulfatase [AslA (VF0238)] [Escherichia coli O18:K1:H7 str. RS218]
contig00017	6302	6757	+	csgB	99.8	83.8	NP_460114	(csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00017	4897	5547	-	csgD	100.0	81.1	NP_460113	(csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00017	4062	4478	-	csgF	99.0	81.2	NP_460111	(csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00017	3202	4035	-	csgG	100.0	83.5	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00013	99332	100078	-	entA	100.0	95.7	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00013	100078	100935	-	entB	100.0	98.1	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00013	102569	103756	-	entC	100.0	97.9	NP_752611	(entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00013	118400	119170	+	entD	100.0	95.2	NP_752599	(entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00013	100949	102559	-	entE	100.0	95.5	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00013	110619	114472	-	entF	99.3	95.7	NP_752604	(entF) enterobactin synthase multienzyme complex component ATP-dependent [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00013	105079	106329	-	entS	100.0	95.4	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00001	66390	68289	-	espL1	100.0	97.6	NP_288154	(espL1) Type III secretion system effector espL1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00035	37583	39769	+	espL4	100.0	97.3	NP_290644	(espL4) Type III secretion system effector EspL4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00039	15212	16265	-	espR1	83.7	93.8	NP_287686	(espR1) Type III secretion system effector espR1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00010	25291	26425	-	espR4	99.5	84.3	NP_288396	(espR4) Type III secretion system effector espR4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00002	203385	204806	+	espX1	100.0	93.2	NP_285716	(espX1) Type III secretion system effector EspX1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00035	7787	9367	-	espX4	99.9	93.2	NP_290672	(espX4) Type III secretion system effector EspX4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00034	31354	32646	+	espX5	100.0	97.1	NP_290699	(espX5) Type III secretion system effector EspX5 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00002	164424	165235	-	espY1	99.9	87.0	NP_285753	(espY1) Type III secretion system effector EspY1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00005	206649	210897	-	fdeC	99.9	94.2	YP_002390132	(fdeC) adhesin FdeC [FdeC (VF0506)] [Escherichia coli O45:K1:H7 str. S88]
contig00013	116135	118375	+	fepA	100.0	96.7	NP_752600	(fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00013	104119	105075	+	fepB	100.0	97.5	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00013	108430	109245	+	fepC	100.0	97.3	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00013	106428	107444	+	fepD	100.0	96.1	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00013	107441	108433	+	fepG	100.0	94.0	NP_752607	(fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00013	114690	115892	-	fes	100.0	96.7	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00047	25238	25849	-	fimA	100.0	88.6	NP_757241	(fimA) Type-1 fimbrial protein A chain precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00047	27347	27949	-	fimB	100.0	98.2	NP_757239	(fimB) Type 1 fimbriae Regulatory protein fimB [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00047	23872	24597	-	fimC	100.0	98.9	NP_757243	(fimC) Chaperone protein fimC precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00047	21169	23805	-	fimD	100.0	98.6	NP_757244	(fimD) Outer membrane usher protein fimD precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00047	26276	26870	-	fimE	99.7	99.3	NP_757240	(fimE) Type 1 fimbriae Regulatory protein fimE [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00047	20629	21162	-	fimF	100.0	97.9	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00047	20113	20616	-	fimG	100.0	97.8	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00047	19191	20102	-	fimH	100.0	97.4	NP_757248	(fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00047	24634	25173	-	fimI	100.0	98.7	NP_757242	(fimI) Fimbrin-like protein fimI precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00010	86337	88358	+	fyuA	100.0	99.9	NP_405467	(fyuA) pesticin/yersiniabactin receptor protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00014	17738	18568	-	gspC	100.0	94.7	YP_404599	(gspC) general secretion pathway protein C [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00014	15648	17498	-	gspD	100.0	96.1	YP_404600	(gspD) general secretion pathway protein D [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00014	14155	15648	-	gspE	100.0	96.9	YP_404601	(gspE) general secretion pathway protein E [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00014	12956	14155	-	gspF	100.0	96.0	YP_404602	(gspF) general secretion pathway protein F [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00014	12460	12915	-	gspG	100.0	95.0	YP_404603	(gspG) general secretion pathway protein G [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00014	11894	12423	-	gspH	99.8	94.9	YP_404604	(gspH) general secretion pathway protein H [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00014	11526	11897	-	gspI	100.0	95.2	YP_404605	(gspI) general secretion pathway protein I [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00014	10924	11493	-	gspJ	100.0	96.7	YP_404606	(gspJ) general secretion pathway protein J [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00014	9950	10927	-	gspK	100.0	97.0	YP_404607	(gspK) general secretion pathway protein K [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00014	8775	9635	-	gspL	100.0	97.0	YP_404608	(gspL) general secretion pathway protein L [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00014	8237	8659	-	gspM	100.0	98.3	YP_404609	(gspM) general secretion pathway protein M [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00010	73237	82728	+	irp1	100.0	99.3	NP_405471	(irp1) yersiniabactin biosynthetic protein Irp1 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00010	67042	73149	+	irp2	100.0	99.8	NP_405472	(irp2) yersiniabactin biosynthetic protein Irp2 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00004	142713	143753	-	ompA	100.0	98.1	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00054	5439	6192	+	yagV/ecpE	99.7	97.1	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00054	3872	5515	+	yagW/ecpD	100.0	99.1	NP_286007	(yagW/ecpD) polymerized tip adhesin of ECP fibers [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00054	1357	3882	+	yagX/ecpC	100.0	98.8	NP_286008	(yagX/ecpC) E. coli common pilus usher EcpC [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00054	663	1331	+	yagY/ecpB	100.0	97.9	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00054	18	605	+	yagZ/ecpA	100.0	99.2	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00010	65892	66851	+	ybtA	100.0	99.5	NP_405473	(ybtA) transcriptional regulator YbtA [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00010	84629	86206	+	ybtE	100.0	99.8	NP_405468	(ybtE) yersiniabactin siderophore biosynthetic protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00010	63923	65725	-	ybtP	100.0	99.6	NP_405474	(ybtP) lipoprotein inner membrane ABC-transporter [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00010	62134	63936	-	ybtQ	100.0	99.7	NP_405475	(ybtQ) inner membrane ABC-transporter YbtQ [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00010	59529	60833	-	ybtS	100.0	99.9	NP_405477	(ybtS) salicylate synthase Irp9 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00010	83822	84625	+	ybtT	100.0	99.8	NP_405469	(ybtT) yersiniabactin biosynthetic protein YbtT [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00010	82725	83825	+	ybtU	100.0	100.0	NP_405470	(ybtU) yersiniabactin biosynthetic protein YbtU [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00010	60861	62141	-	ybtX	100.0	99.7	NP_405476	(ybtX) putative signal transducer [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00005	213919	214509	+	ykgK/ecpR	100.0	97.0	NP_286011	(ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

ID282

Contig	Start	End	Strand	Gene	Coverage	Identity	Accession	Product
contig00334	234	1662	+	aslA	100.0	97.2	AAG10151	(aslA) putative arylsulfatase [AslA (VF0238)] [Escherichia coli O18:K1:H7 str. RS218]
contig00022	14462	15490	-	chuS	100.0	96.2	NP_756169	(chuS) heme oxygenase ChuS [Chu (VF0227)] [Escherichia coli CFT073]
contig00022	21655	22647	+	chuU	100.0	98.6	NP_756179	(chuU) heme permease protein ChuU [Chu (VF0227)] [Escherichia coli CFT073]
contig00022	22614	23414	+	chuV	100.0	98.9	NP_756180	(chuV) ATP-binding hydrophilic protein ChuV [Chu (VF0227)] [Escherichia coli CFT073]
contig00022	19139	20476	+	chuW	100.0	96.7	NP_756176	(chuW) Putative oxygen independent coproporphyrinogen III oxidase [Chu (VF0227)] [Escherichia coli CFT073]
contig00022	20983	21606	+	chuY	100.0	97.0	NP_756178	(chuY) ChuY [Chu (VF0227)] [Escherichia coli CFT073]
contig00289	4713	5168	-	csgB	99.8	83.6	NP_460114	(csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00809	906	1322	+	csgF	99.0	81.0	NP_460111	(csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00809	1349	2182	+	csgG	100.0	83.3	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00063	9706	10452	-	entA	100.0	96.0	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig01116	792	1538	+	entA	100.0	95.7	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00063	10452	11309	-	entB	100.0	98.4	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig01116	1	792	+	entB	92.3	98.1	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00063	12943	13992	-	entC	88.4	96.6	NP_752611	(entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00480	2332	3102	+	entD	100.0	92.1	NP_752599	(entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00672	106	876	-	entD	100.0	94.3	NP_752599	(entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00063	11323	12933	-	entE	100.0	96.6	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00095	1277	5130	+	entF	99.3	95.4	NP_752604	(entF) enterobactin synthase multienzyme complex component ATP-dependent [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00095	9420	10670	+	entS	100.0	95.8	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00507	1173	2423	-	entS	100.0	95.4	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00341	1109	3007	-	espL1	100.0	96.7	NP_288154	(espL1) Type III secretion system effector espL1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00429	1098	3284	+	espL4	100.0	97.0	NP_290644	(espL4) Type III secretion system effector EspL4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00168	2406	3656	+	espR1	99.3	94.2	NP_287686	(espR1) Type III secretion system effector espR1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00091	9493	10601	-	espR4	97.2	84.4	NP_288396	(espR4) Type III secretion system effector espR4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00093	4108	5529	+	espX1	100.0	95.7	NP_285716	(espX1) Type III secretion system effector EspX1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00170	2864	4444	+	espX4	100.0	96.3	NP_290672	(espX4) Type III secretion system effector EspX4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00523	2211	3791	+	espX4	99.9	93.3	NP_290672	(espX4) Type III secretion system effector EspX4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00306	4129	5421	+	espX5	100.0	96.0	NP_290699	(espX5) Type III secretion system effector EspX5 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00531	2325	3617	+	espX5	100.0	95.7	NP_290699	(espX5) Type III secretion system effector EspX5 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00336	847	1568	+	espY1	95.9	88.6	NP_285753	(espY1) Type III secretion system effector EspY1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00056	12424	12974	+	espY2	96.5	88.0	NP_285765	(espY2) Type III secretion system effector EspY2 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00371	2798	4369	+	espY3	100.0	95.7	NP_286160	(espY3) Type III secretion system effector EspY3 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00041	844	3252	-	espY4	100.0	96.3	NP_290352	(espY4) Type III secretion system effector EspY4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00029	2142	6383	-	fdeC	99.8	92.7	YP_002390132	(fdeC) adhesin FdeC [FdeC (VF0506)] [Escherichia coli O45:K1:H7 str. S88]
contig00400	247	4495	+	fdeC	99.9	94.2	YP_002390132	(fdeC) adhesin FdeC [FdeC (VF0506)] [Escherichia coli O45:K1:H7 str. S88]
contig00480	67	2307	+	fepA	100.0	96.8	NP_752600	(fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00672	901	3141	-	fepA	100.0	96.8	NP_752600	(fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00095	10674	11630	-	fepB	100.0	97.9	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00507	213	1169	+	fepB	100.0	97.5	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00095	6504	7319	-	fepC	100.0	96.8	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00757	1931	2746	-	fepC	100.0	97.3	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00095	8305	9321	-	fepD	100.0	96.2	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00507	2522	3538	+	fepD	100.0	96.2	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00095	7316	8308	-	fepG	100.0	94.3	NP_752607	(fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00095	1	1059	+	fes	88.0	96.5	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00605	1	1059	+	fes	88.0	96.2	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00719	2476	3051	-	fimA	95.0	91.8	NP_757241	(fimA) Type-1 fimbrial protein A chain precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig01198	112	723	+	fimA	100.0	88.1	NP_757241	(fimA) Type-1 fimbrial protein A chain precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00015	1113	1715	-	fimB	100.0	98.2	NP_757239	(fimB) Type 1 fimbriae Regulatory protein fimB [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00719	1110	1835	-	fimC	100.0	98.5	NP_757243	(fimC) Chaperone protein fimC precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00015	39	635	-	fimE	100.0	98.7	NP_757240	(fimE) Type 1 fimbriae Regulatory protein fimE [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00990	355	888	-	fimF	100.0	97.4	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00719	1872	2411	-	fimI	100.0	98.3	NP_757242	(fimI) Fimbrin-like protein fimI precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig01198	788	1327	+	fimI	100.0	98.3	NP_757242	(fimI) Fimbrin-like protein fimI precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00004	33372	35393	+	fyuA	100.0	100.0	NP_405467	(fyuA) pesticin/yersiniabactin receptor protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00001	27548	28378	-	gspC	100.0	94.5	YP_404599	(gspC) general secretion pathway protein C [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	25458	27308	-	gspD	100.0	96.3	YP_404600	(gspD) general secretion pathway protein D [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	23965	25458	-	gspE	100.0	95.3	YP_404601	(gspE) general secretion pathway protein E [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	22766	23965	-	gspF	100.0	94.1	YP_404602	(gspF) general secretion pathway protein F [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	22270	22725	-	gspG	100.0	95.6	YP_404603	(gspG) general secretion pathway protein G [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	21703	22233	-	gspH	100.0	95.9	YP_404604	(gspH) general secretion pathway protein H [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	21335	21706	-	gspI	100.0	92.5	YP_404605	(gspI) general secretion pathway protein I [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	20733	21302	-	gspJ	100.0	94.6	YP_404606	(gspJ) general secretion pathway protein J [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	19759	20736	-	gspK	100.0	96.8	YP_404607	(gspK) general secretion pathway protein K [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	18584	19444	-	gspL	100.0	93.7	YP_404608	(gspL) general secretion pathway protein L [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00001	18047	18468	-	gspM	99.8	92.9	YP_404609	(gspM) general secretion pathway protein M [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00025	3924	5086	+	iroB	99.9	98.4	NP_753168	(iroB) glucosyltransferase IroB [Salmochelin (IA013)] [Escherichia coli CFT073]
contig00025	5149	8886	+	iroC	100.0	99.1	NP_753167	(iroC) ATP binding cassette transporter [Salmochelin (IA013)] [Escherichia coli CFT073]
contig00025	8990	10219	+	iroD	100.0	98.5	NP_753166	(iroD) esterase [Salmochelin (IA013)] [Escherichia coli CFT073]
contig00025	10304	11260	+	iroE	100.0	99.5	NP_753165	(iroE) esterase [Salmochelin (IA013)] [Escherichia coli CFT073]
contig00025	11305	13482	-	iroN	100.0	99.1	NP_753164	(iroN) salmochelin receptor IroN [IroN (VF0230)] [Escherichia coli CFT073]
contig00004	20272	29763	+	irp1	100.0	99.7	NP_405471	(irp1) yersiniabactin biosynthetic protein Irp1 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00004	14077	20184	+	irp2	100.0	99.5	NP_405472	(irp2) yersiniabactin biosynthetic protein Irp2 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00082	4463	6250	+	iucA	100.0	94.3	NP_755502	(iucA) aerobactin siderophore biosynthesis protein IucD [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00082	6251	7198	+	iucB	100.0	95.7	NP_755501	(iucB) aerobactin siderophore biosynthesis protein IucB [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00082	7198	8940	+	iucC	100.0	96.0	NP_755500	(iucC) aerobactin siderophore biosynthesis protein IucC [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00082	8937	10258	+	iucD	98.8	96.3	NP_755499	(iucD) L-lysine 6-monooxygenase IucD [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00082	10196	12497	+	iutA	100.0	88.4	NP_755498	(iutA) ferric aerobactin receptor precusor IutA [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00673	2232	3200	-	ompA	93.1	99.1	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00022	15539	17521	-	shuA	100.0	98.1	YP_405019	(shuA) outer membrane heme/hemoglobin receptor ShuA [Shu (VF0256)] [Shigella dysenteriae Sd197]
contig00022	18127	19119	+	shuT	100.0	98.3	YP_405017	(shuT) periplasmic binding protein ShuT [Shu (VF0256)] [Shigella dysenteriae Sd197]
contig00022	20489	20983	+	shuX	100.0	96.4	YP_405016	(shuX) shu locus protein ShuX [Shu (VF0256)] [Shigella dysenteriae Sd197]
contig00629	494	1247	+	yagV/ecpE	99.7	97.2	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00029	17739	20264	+	yagX/ecpC	100.0	97.9	NP_286008	(yagX/ecpC) E. coli common pilus usher EcpC [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00589	571	3096	+	yagX/ecpC	100.0	98.7	NP_286008	(yagX/ecpC) E. coli common pilus usher EcpC [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00029	17045	17713	+	yagY/ecpB	100.0	98.4	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00589	1	545	+	yagY/ecpB	81.5	99.1	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00029	16400	16987	+	yagZ/ecpA	100.0	98.8	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00004	12926	13885	+	ybtA	100.0	99.3	NP_405473	(ybtA) transcriptional regulator YbtA [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00004	31664	33241	+	ybtE	100.0	99.9	NP_405468	(ybtE) yersiniabactin siderophore biosynthetic protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00004	10957	12759	-	ybtP	100.0	99.7	NP_405474	(ybtP) lipoprotein inner membrane ABC-transporter [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00004	9168	10970	-	ybtQ	100.0	99.8	NP_405475	(ybtQ) inner membrane ABC-transporter YbtQ [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00004	6563	7867	-	ybtS	100.0	99.8	NP_405477	(ybtS) salicylate synthase Irp9 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00004	30857	31660	+	ybtT	100.0	99.8	NP_405469	(ybtT) yersiniabactin biosynthetic protein YbtT [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00004	29760	30860	+	ybtU	100.0	99.6	NP_405470	(ybtU) yersiniabactin biosynthetic protein YbtU [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00004	7895	9175	-	ybtX	100.0	99.6	NP_405476	(ybtX) putative signal transducer [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00029	15735	16325	+	ykgK/ecpR	100.0	99.0	NP_286011	(ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig01624	206	796	+	ykgK/ecpR	100.0	97.1	NP_286011	(ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

ORTHO013EI

Contig	Start	End	Strand	Gene	Coverage	Identity	Accession	Product
contig00083	391	505	-	astA	98.3	91.3	BAA94855	(astA) heat-stable enterotoxin 1 [EAST1 (VF0216)] [Escherichia coli O44:H18 042]
contig00001	6192	7025	-	csgG	100.0	81.7	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00006	15401	15937	-	lpfA	100.0	89.2	NP_462541	(lpfA) long polar fimbria protein LpfA [Lpf (VF0105)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00006	14617	15315	-	lpfB	100.0	89.1	NP_462540	(lpfB) long polar fimbrial chaperone protein LpfB [Lpf (VF0105)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00006	12066	14594	-	lpfC	100.0	90.1	NP_462539	(lpfC) long polar fimbrial usher protein LpfC [Lpf (VF0105)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00006	10439	10966	-	lpfE	100.0	83.3	NP_462537	(lpfE) long polar fimbrial minor subunit LpfE adhesin [Lpf (VF0105)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00055	11527	12572	+	ompA	99.0	84.7	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]

ORTHO055E

Contig	Start	End	Strand	Gene	Coverage	Identity	Accession	Product
contig00192	6014	6865	-	entB	99.3	82.4	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00031	9	1079	-	ompA	100.0	83.1	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00250	360	1113	-	yagV/ecpE	99.7	84.2	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00250	1039	2682	-	yagW/ecpD	100.0	88.1	NP_286007	(yagW/ecpD) polymerized tip adhesin of ECP fibers [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00250	2672	5197	-	yagX/ecpC	100.0	86.6	NP_286008	(yagX/ecpC) E. coli common pilus usher EcpC [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00250	5223	5891	-	yagY/ecpB	100.0	88.0	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00250	5953	6536	-	yagZ/ecpA	99.3	89.9	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

ORTHO082EI

Contig	Start	End	Strand	Gene	Coverage	Identity	Accession	Product
contig00004	31278	31772	+	chuX	100.0	82.4	NP_756177	(chuX) putative heme-binding protein ChuX [Chu (VF0227)] [Escherichia coli CFT073]
contig00006	183570	184028	-	csgB	100.0	81.7	NP_460114	(csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00006	184790	185440	+	csgD	100.0	83.7	NP_460113	(csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00006	185445	185837	+	csgE	99.2	82.8	NP_460112	(csgE) curli production assembly/transport protein CsgE [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00006	185863	186276	+	csgF	99.3	81.1	NP_460111	(csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00006	186302	187135	+	csgG	99.8	82.3	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00002	204677	205534	-	entB	100.0	80.9	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00002	205548	207158	-	entE	99.9	81.5	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00002	212909	213696	+	fepC	96.6	80.8	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00011	83922	84907	+	fliG	99.3	80.0	YP_001006742	(fliG) flagellar motor switch protein G [Flagella (VF0394)] [Yersinia enterocolitica subsp. enterocolitica 8081]
contig00013	61710	62756	+	ompA	99.5	88.6	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]

ORTHO08HW

Contig	Start	End	Strand	Gene	Coverage	Identity	Accession	Product
contig00016	28623	31667	-	cnf1	100.0	99.9	CAA50007	(cnf1) cytotoxic necrotizing factor 1 [CNF-1 (VF0240)] [Escherichia coli str. E-B35]
contig00017	97772	98227	-	csgB	99.8	83.8	NP_460114	(csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00017	98981	99631	+	csgD	100.0	81.0	NP_460113	(csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00017	100050	100466	+	csgF	99.0	81.2	NP_460111	(csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00017	100493	101326	+	csgG	100.0	83.0	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00005	212523	213269	+	entA	100.0	96.0	NP_752614	(entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00005	211666	212523	+	entB	100.0	97.9	NP_752613	(entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00005	208845	210032	+	entC	100.0	97.5	NP_752611	(entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00005	193431	194201	-	entD	100.0	95.1	NP_752599	(entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00005	210042	211652	+	entE	100.0	95.8	NP_752612	(entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00005	198129	201958	+	entF	98.7	95.5	NP_752604	(entF) enterobactin synthase multienzyme complex component ATP-dependent [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00005	206272	207522	+	entS	100.0	95.5	NP_752609	(entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00001	197211	199080	-	espL1	98.5	95.2	NP_288154	(espL1) Type III secretion system effector espL1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00037	25977	27031	+	espR1	83.7	94.2	NP_287686	(espR1) Type III secretion system effector espR1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00003	127936	129356	+	espX1	99.9	94.6	NP_285716	(espX1) Type III secretion system effector EspX1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00026	46399	47979	+	espX4	99.9	92.9	NP_290672	(espX4) Type III secretion system effector EspX4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00038	5831	7123	-	espX5	100.0	95.6	NP_290699	(espX5) Type III secretion system effector EspX5 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00027	45881	50129	-	fdeC	99.9	94.2	YP_002390132	(fdeC) adhesin FdeC [FdeC (VF0506)] [Escherichia coli O45:K1:H7 str. S88]
contig00005	194226	196466	-	fepA	100.0	97.5	NP_752600	(fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00005	207526	208482	-	fepB	100.0	97.4	NP_752610	(fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00005	203356	204171	-	fepC	100.0	97.3	NP_752606	(fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00005	205157	206173	-	fepD	100.0	96.4	NP_752608	(fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00005	204168	205160	-	fepG	100.0	94.5	NP_752607	(fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00005	196709	197911	+	fes	100.0	96.4	NP_752602	(fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00003	244191	244796	-	fimA	100.0	90.1	NP_757241	(fimA) Type-1 fimbrial protein A chain precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00003	246294	246896	-	fimB	100.0	97.8	NP_757239	(fimB) Type 1 fimbriae Regulatory protein fimB [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00003	242825	243550	-	fimC	100.0	98.3	NP_757243	(fimC) Chaperone protein fimC precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00003	240122	242758	-	fimD	100.0	98.6	NP_757244	(fimD) Outer membrane usher protein fimD precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00003	245220	245816	-	fimE	100.0	99.0	NP_757240	(fimE) Type 1 fimbriae Regulatory protein fimE [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00003	239582	240115	-	fimF	100.0	97.4	NP_757245	(fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00003	239066	239569	-	fimG	100.0	98.4	NP_757247	(fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00003	238144	239055	-	fimH	100.0	97.3	NP_757248	(fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00003	243587	244126	-	fimI	100.0	98.9	NP_757242	(fimI) Fimbrin-like protein fimI precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00011	118814	120835	+	fyuA	100.0	100.0	NP_405467	(fyuA) pesticin/yersiniabactin receptor protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00023	4011	4988	-	gspK	100.0	97.7	YP_404607	(gspK) general secretion pathway protein K [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00023	2836	3696	-	gspL	100.0	96.9	YP_404608	(gspL) general secretion pathway protein L [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00023	2298	2720	-	gspM	100.0	97.2	YP_404609	(gspM) general secretion pathway protein M [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00016	36262	39336	-	hlyA	100.0	97.4	NP_755445	(hlyA) Hemolysin A [Hemolysin (VF0225)] [Escherichia coli CFT073]
contig00016	34068	36191	-	hlyB	100.0	99.2	NP_755448	(hlyB) Hemolysin B [Hemolysin (VF0225)] [Escherichia coli CFT073]
contig00016	39348	40022	-	hlyC	100.0	99.6	NP_755444	(hlyC) Hemolysin C [Hemolysin (VF0225)] [Escherichia coli CFT073]
contig00016	32613	34049	-	hlyD	100.0	99.9	NP_755449	(hlyD) Hemolysin D [Hemolysin (VF0225)] [Escherichia coli CFT073]
contig00011	105714	115205	+	irp1	100.0	99.8	NP_405471	(irp1) yersiniabactin biosynthetic protein Irp1 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00011	99519	105626	+	irp2	100.0	99.8	NP_405472	(irp2) yersiniabactin biosynthetic protein Irp2 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00052	7018	8805	+	iucA	100.0	94.3	NP_755502	(iucA) aerobactin siderophore biosynthesis protein IucD [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00052	8806	9753	+	iucB	100.0	95.6	NP_755501	(iucB) aerobactin siderophore biosynthesis protein IucB [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00052	9753	11495	+	iucC	100.0	96.1	NP_755500	(iucC) aerobactin siderophore biosynthesis protein IucC [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00052	11492	12813	+	iucD	98.8	96.3	NP_755499	(iucD) L-lysine 6-monooxygenase IucD [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00052	12751	15052	+	iutA	100.0	88.4	NP_755498	(iutA) ferric aerobactin receptor precusor IutA [Aerobactin (VF0229)] [Escherichia coli CFT073]
contig00008	104057	105109	-	ompA	100.0	94.5	AAF37887	(ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00016	9953	10265	-	papB	99.4	99.4		(papB) regulatory protein PapB [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig00016	5979	8501	-	papC	100.0	99.7	NP_755465	(papC) usher protein PapC [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig00016	5174	5779	-	papD	100.0	99.8	NP_755464	(papD) chaperone protein PapD [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig00016	3462	4001	-	papE	100.0	94.1	NP_755460	(papE) P pilus minor subunit PapE [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig00016	2883	3417	-	papF	100.0	94.4	NP_755459	(papF) P pilus minor subunit PapF [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig00016	8548	9135	-	papH	100.0	98.3	NP_755466	(papH) P pilus termination subunit PapH [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig00016	10670	10903	+	papI	100.0	94.4	NP_755468	(papI) regulatory protein PapI [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig00016	4556	5137	-	papJ	100.0	100.0	NP_755463	(papJ) P pilus assembly protein PapJ [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig00016	4010	4549	-	papK	100.0	99.4	NP_755461	(papK) P pilus minor subunit PapK [P fimbriae (VF0220)] [Escherichia coli CFT073]
contig00016	1018	1569	-	papX	100.0	97.5	NP_755457	(papX) PapX protein regulates flagellum synthesis to repress motility [P fimbriae (CVF425)] [Escherichia coli CFT073]
contig00027	59235	59988	+	yagV/ecpE	99.7	96.8	NP_286006	(yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00027	57668	59311	+	yagW/ecpD	100.0	98.7	NP_286007	(yagW/ecpD) polymerized tip adhesin of ECP fibers [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00027	55153	57678	+	yagX/ecpC	100.0	98.7	NP_286008	(yagX/ecpC) E. coli common pilus usher EcpC [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00027	54459	55127	+	yagY/ecpB	100.0	98.8	NP_286009	(yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00027	53814	54401	+	yagZ/ecpA	100.0	99.3	NP_286010	(yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00011	98369	99328	+	ybtA	100.0	99.8	NP_405473	(ybtA) transcriptional regulator YbtA [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00011	117106	118683	+	ybtE	100.0	99.8	NP_405468	(ybtE) yersiniabactin siderophore biosynthetic protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00011	96400	98202	-	ybtP	100.0	99.7	NP_405474	(ybtP) lipoprotein inner membrane ABC-transporter [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00011	94611	96413	-	ybtQ	100.0	99.9	NP_405475	(ybtQ) inner membrane ABC-transporter YbtQ [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00011	92006	93310	-	ybtS	100.0	97.6	NP_405477	(ybtS) salicylate synthase Irp9 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00011	116299	117102	+	ybtT	100.0	99.8	NP_405469	(ybtT) yersiniabactin biosynthetic protein YbtT [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00011	115202	116302	+	ybtU	100.0	99.7	NP_405470	(ybtU) yersiniabactin biosynthetic protein YbtU [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00011	93338	94618	-	ybtX	100.0	97.7	NP_405476	(ybtX) putative signal transducer [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00027	53149	53739	+	ykgK/ecpR	100.0	97.3	NP_286011	(ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]

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Multi-Locus Sequence Typing (MLST)

Symbol	Meaning
~	novel full length allele similar to match
?	partial match to known allele
-	allele missing

	Scheme	ST	1	2	3	4	5	6	7
ID002	ecloacae	826	dnaA(261)	fusA(171)	gyrB(282)	leuS(316)	pyrG(49)	rplB(12)	rpoB(26)
ID003	ecoli	38	adk(4)	fumC(26)	gyrB(2)	icd(25)	mdh(5)	purA(5)	recA(19)
ID005	ecoli	-	adk(4)	fumC(26)	gyrB(2)	icd(25)	mdh(455)	purA(5)	recA(19)
ID006	ecoli	398	adk(64)	fumC(7)	gyrB(1)	icd(1)	mdh(8)	purA(8)	recA(6)
ID007I	ecoli	131	adk(53)	fumC(40)	gyrB(47)	icd(13)	mdh(36)	purA(28)	recA(29)
ID011	ecoli	131	adk(53)	fumC(40)	gyrB(47)	icd(13)	mdh(36)	purA(28)	recA(29)
ID013I	ecoli	131	adk(53)	fumC(40)	gyrB(47)	icd(13)	mdh(36)	purA(28)	recA(29)
ID016I	cfreundii	-	aspC(163,171)	clpX(112,193)	fadD(112,199)	mdh(13,172)	arcA(94,111)	dnaG(84,154)	lysP(169)
ID017	ecoli	3580	adk(6)	fumC(65)	gyrB(344)	icd(1)	mdh(11)	purA(13)	recA(6)
ID018CT	ecoli	695	adk(10)	fumC(11)	gyrB(4)	icd(12)	mdh(8)	purA(18)	recA(2)
ID019	ecoli	542	adk(112)	fumC(11)	gyrB(5)	icd(12)	mdh(8)	purA(8)	recA(86)
ID01CT	ecoli	48	adk(6)	fumC(11)	gyrB(4)	icd(8)	mdh(8)	purA(8)	recA(2)
ID021	ecoli	167	adk(10)	fumC(11)	gyrB(4)	icd(8)	mdh(8)	purA(13)	recA(2)
ID027	ecoli	10	adk(10)	fumC(11)	gyrB(4)	icd(8)	mdh(8)	purA(8)	recA(2)
ID031	cfreundii	-	aspC(171)	clpX(193)	fadD(112)	mdh(172)	arcA(114)	dnaG(84)	lysP(~101)
ID034I	ecoli	10	adk(10)	fumC(11)	gyrB(4)	icd(8)	mdh(8)	purA(8)	recA(2)
ID041	ecoli	2797	adk(203)	fumC(26)	gyrB(27)	icd(27)	mdh(40)	purA(5)	recA(73)
ID043I	ecoli	617	adk(10)	fumC(11)	gyrB(4)	icd(8)	mdh(8)	purA(13)	recA(73)
ID044	ecoli	167	adk(10)	fumC(11)	gyrB(4)	icd(8)	mdh(8)	purA(13)	recA(2)
ID046II	senterica	-	aroC(~622)	dnaN(559)	hemD(496?)	hisD(~764)	purE(~690)	sucA(281)	thrA(636)
ID049	ecoli	1312	adk(6)	fumC(11)	gyrB(4)	icd(8)	mdh(8)	purA(78)	recA(2)
ID051	ecoli	131	adk(53)	fumC(40)	gyrB(47)	icd(13)	mdh(36)	purA(28)	recA(29)
ID054	ecoli	2852	adk(6)	fumC(65)	gyrB(5)	icd(1)	mdh(11)	purA(13)	recA(6)
ID057	ecoli	410	adk(6)	fumC(4)	gyrB(12)	icd(1)	mdh(20)	purA(18)	recA(7)
ID066II	senterica	-	aroC(~620)	dnaN(559)	hemD(494)	hisD(759?)	purE(690?)	sucA(581)	thrA(636)
ID067	ecoli	1421	adk(8)	fumC(7)	gyrB(1)	icd(8)	mdh(8)	purA(8)	recA(2)
ID068	ecoli	10	adk(10)	fumC(11)	gyrB(4)	icd(8)	mdh(8)	purA(8)	recA(2)
ID073I	ecoli	1421	adk(8)	fumC(7)	gyrB(1)	icd(8)	mdh(8)	purA(8)	recA(2)
ID077	ecoli	2852	adk(6)	fumC(65)	gyrB(5)	icd(1)	mdh(11)	purA(13)	recA(6)
ID081I	ecoli	540	adk(6)	fumC(7)	gyrB(57)	icd(1)	mdh(8)	purA(8)	recA(2)
ID086II	ecoli	131	adk(53)	fumC(40)	gyrB(47)	icd(13)	mdh(36)	purA(28)	recA(29)
ID088	ecoli	1284	adk(10)	fumC(4)	gyrB(4)	icd(8)	mdh(8)	purA(13)	recA(73)
ID092	abaumannii_2	103	Pas_cpn60(7)	Pas_fusA(3)	Pas_gltA(2)	Pas_pyrG(1)	Pas_recA(7)	Pas_rplB(1)	Pas_rpoB(4)
ID094LLFII	ecoli	-	adk(4)	fumC(26)	gyrB(10)	icd(25)	mdh(5)	purA(5)	recA(594?)
ID099	ecoli	3580	adk(6)	fumC(65)	gyrB(344)	icd(1)	mdh(11)	purA(13)	recA(6)
ID09CT	ecoli	711	adk(9)	fumC(6)	gyrB(15)	icd(131)	mdh(24)	purA(7)	recA(7)
ID101	ecoli	3580	adk(6)	fumC(65)	gyrB(344)	icd(1)	mdh(11)	purA(13)	recA(6)
ID107II	ecoli	648	adk(92)	fumC(4)	gyrB(87)	icd(96)	mdh(70)	purA(58)	recA(2)
ID124	ecoli	167	adk(10)	fumC(11)	gyrB(4)	icd(8)	mdh(8)	purA(13)	recA(2)
ID127	ecoli	167	adk(10)	fumC(11)	gyrB(4)	icd(8)	mdh(8)	purA(13)	recA(2)
ID128	ecoli	131	adk(53)	fumC(40)	gyrB(47)	icd(13)	mdh(36)	purA(28)	recA(29)
ID129E	ecoli	351	adk(6)	fumC(95)	gyrB(4)	icd(88)	mdh(7)	purA(7)	recA(7)
ID130	ecoli	3897	adk(10)	fumC(7)	gyrB(4)	icd(8)	mdh(12)	purA(8)	recA(7)
ID134	senterica	-	aroC(621)	dnaN(559)	hemD(552)	hisD(765?)	purE(617)	sucA(281)	thrA(695?)
ID136	ecoli	2852	adk(6)	fumC(65)	gyrB(5)	icd(1)	mdh(11)	purA(13)	recA(6)
ID141	-	-
ID142	kpneumoniae	-	gapA(242?)	infB(45)	mdh(21)	pgi(49)	phoE(-)	rpoB(22)	tonB(-)
ID164	ecoli	617	adk(10)	fumC(11)	gyrB(4)	icd(8)	mdh(8)	purA(13)	recA(73)
ID169	ecoli	131	adk(53)	fumC(40)	gyrB(47)	icd(13)	mdh(36)	purA(28)	recA(29)
ID177	ecoli	38	adk(4)	fumC(26)	gyrB(2)	icd(25)	mdh(5)	purA(5)	recA(19)
ID178	ecoli	648	adk(92)	fumC(4)	gyrB(87)	icd(96)	mdh(70)	purA(58)	recA(2)
ID182	ecoli	746	adk(10)	fumC(7)	gyrB(4)	icd(8)	mdh(12)	purA(8)	recA(2)
ID186	ecoli	3580	adk(6)	fumC(65)	gyrB(344)	icd(1)	mdh(11)	purA(13)	recA(6)
ID187	ecoli	5455	adk(10)	fumC(27)	gyrB(5)	icd(8)	mdh(12)	purA(8)	recA(2)
ID195	ecoli	711	adk(9)	fumC(6)	gyrB(15)	icd(131)	mdh(24)	purA(7)	recA(7)
ID197	ecoli	617	adk(10)	fumC(11)	gyrB(4)	icd(8)	mdh(8)	purA(13)	recA(73)
ID199	ecoli	224	adk(6)	fumC(4)	gyrB(33)	icd(16)	mdh(11)	purA(8)	recA(6)
ID208	ecoli	648	adk(92)	fumC(4)	gyrB(87)	icd(96)	mdh(70)	purA(58)	recA(2)
ID214	ecoli	617	adk(10)	fumC(11)	gyrB(4)	icd(8)	mdh(8)	purA(13)	recA(73)
ID224	ecoli	167	adk(10)	fumC(11)	gyrB(4)	icd(8)	mdh(8)	purA(13)	recA(2)
ID228	ecoli	131	adk(53)	fumC(40)	gyrB(47)	icd(13)	mdh(36)	purA(28)	recA(29)
ID229	ecoli	3580	adk(6)	fumC(65)	gyrB(344)	icd(1)	mdh(11)	purA(13)	recA(6)
ID231	ecoli	2852	adk(6)	fumC(65)	gyrB(5)	icd(1)	mdh(11)	purA(13)	recA(6)
ID233	kpneumoniae	-	gapA(16)	infB(18)	mdh(21)	pgi(27)	phoE(57)	rpoB(22)	tonB(564?)
ID235	ecoli	648	adk(92)	fumC(4)	gyrB(87)	icd(96)	mdh(70)	purA(58)	recA(2)
ID237	ecoli	3580	adk(6)	fumC(65)	gyrB(344)	icd(1)	mdh(11)	purA(13)	recA(6)
ID256	ecoli	131	adk(53)	fumC(40)	gyrB(47)	icd(13)	mdh(36)	purA(28)	recA(29)
ID263	ecoli	167	adk(10)	fumC(11)	gyrB(4)	icd(8)	mdh(8)	purA(13)	recA(2)
ID282	senterica	-	aroC(620)	dnaN(558,559)	hemD(492)	hisD(~763)	purE(614)	sucA(580)	thrA(636?)
ORTHO013EI	ecloacae	-	dnaA(~144)	fusA(106)	gyrB(~330)	leuS(237)	pyrG(~298)	rplB(12)	rpoB(148)
ORTHO055E	kpneumoniae	-	gapA(18)	infB(22)	mdh(18)	pgi(186)	phoE(25)	rpoB(37)	tonB(51)
ORTHO082EI	cfreundii	116	aspC(16)	clpX(12)	fadD(7)	mdh(10)	arcA(5)	dnaG(55)	lysP(5)
ORTHO08HW	ecoli	410	adk(6)	fumC(4)	gyrB(12)	icd(1)	mdh(20)	purA(18)	recA(7)

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Pangenome Analysis

Pangenome genes summary

Genes	Description	Number
Core genes	(99% <= strains <= 100%)	0
Soft core genes	(95% <= strains < 99%)	4
Shell genes	(15% <= strains < 95%)	6073
Cloud genes	(0% <= strains < 15%)	45883
Total genes	(0% <= strains <= 100%)	51960

Schematic representation of genes presence (color) or absence (blank) between samples:

Pangenome tree based on presence/absence of accessory genes representation

Rectangular (phylogram)

Circular (phylogram)

Circular (cladogram)

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WARNING: Core genome alignment tree was not generated during pangenome analysis. Please check.

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Insertion sequence characterization

Field	Description
Region	Numeric code given to insertion sequence (IS)
Orientation	The orientation of IS position: Either forward (F) or reverse (F)
X-cordinates	The left coordinate of the position
Y-coordinates	The right coordinate of the position
Gap	The distance between the x and y coordinates
CallType	Describes whether a position hit is novel (not in reference) or known (in the reference)
LeftGene	Locus tag ID of the gene closest to the left side of the IS position
LeftGeneDescription	Description of the gene feature from the left side of the IS position. By default this is the product position
RightGene	Locus tag ID of the gene closest to the right side of the IS position
RightGeneDescription	Description of the gene feature from the right side of the IS position. By default this is the product position

Select the sample

ID005

Region	Orientation	X-coordinates	Y-coordinates	Gap	CallType	LeftGene	LeftGeneDescription	RightGene	RightGeneDescription
region_1	R	-1	319814	319815	novel	b4403	putative rRNA methyltransferase	b0304	putative pyridine nucleotide-disulfide oxidoreductase RclA
region_2	R	-1	3583424	3583425	novel	b4403	putative rRNA methyltransferase	b3443	putative uncharacterized protein YrhA

ID007I

Region	Orientation	X-coordinates	Y-coordinates	Gap	CallType	LeftGene	LeftGeneDescription	RightGene	RightGeneDescription
region_1	R	1090327	1090328	1	novel	b1024	partially deacetylated poly-beta-1,6-N-acetyl-D-glucosamine outer membrane porin	b1024	partially deacetylated poly-beta-1,6-N-acetyl-D-glucosamine outer membrane porin

ID016I

Region	Orientation	X-coordinates	Y-coordinates	Gap	CallType	LeftGene	LeftGeneDescription	RightGene	RightGeneDescription
region_1	R	1101651	1101964	313	novel*	b1037	curli secretion channel	b1038	curli assembly component

ID017

Region	Orientation	X-coordinates	Y-coordinates	Gap	CallType	LeftGene	LeftGeneDescription	RightGene	RightGeneDescription
region_1	R	-1	2208341	2208342	novel	b4403	putative rRNA methyltransferase	b2121	VWA domain-containing protein YehP

ID027

Region	Orientation	X-coordinates	Y-coordinates	Gap	CallType	LeftGene	LeftGeneDescription	RightGene	RightGeneDescription
region_1	R	-1	3031157	3031158	novel	b4403	putative rRNA methyltransferase	b2888	urate:H(+) symporter

ID031

Region	Orientation	X-coordinates	Y-coordinates	Gap	CallType	LeftGene	LeftGeneDescription	RightGene	RightGeneDescription
region_1	R	1749189	1749199	-10	novel	b1669	conserved protein YdhT	b1669	conserved protein YdhT
region_2	F	2385676	2385685	-9	novel	b2270	IPR002035/DUF3520 domain-containing protein YfbK	b2270	IPR002035/DUF3520 domain-containing protein YfbK

ID043I

Region	Orientation	X-coordinates	Y-coordinates	Gap	CallType	LeftGene	LeftGeneDescription	RightGene	RightGeneDescription
region_1	R	676260	676263	-3	novel	b0644	Sel1 repeat-containing protein YbeQ	b0644	Sel1 repeat-containing protein YbeQ
region_2	F	1577668	1577670	-2	novel	b1496	ABC transporter family protein YddA	b1496	ABC transporter family protein YddA
region_3	F	1581836	1581841	-5	novel	b1498	putative sulfatase	b1498	putative sulfatase
region_4	F	3414053	3414067	-14	novel	b3265	multidrug efflux pump membrane fusion lipoprotein AcrE	b3265	multidrug efflux pump membrane fusion lipoprotein AcrE
region_5	R	3668436	3668445	-9	novel	b3518	cytochrome c peroxidase	b3518	cytochrome c peroxidase

ID044

Region	Orientation	X-coordinates	Y-coordinates	Gap	CallType	LeftGene	LeftGeneDescription	RightGene	RightGeneDescription
region_1	R	-1	2448605	2448606	novel	b4403	putative rRNA methyltransferase	b2331	putative endonuclease SmrB
region_1	R	1474910	1474984	74	novel*	b1406	pyridoxine 4-dehydrogenase	b1406	pyridoxine 4-dehydrogenase
region_2	F	3414017	3414055	38	novel*	b3265	multidrug efflux pump membrane fusion lipoprotein AcrE	b3265	multidrug efflux pump membrane fusion lipoprotein AcrE

ID046II

Region	Orientation	X-coordinates	Y-coordinates	Gap	CallType	LeftGene	LeftGeneDescription	RightGene	RightGeneDescription
region_1	F	20094	20168	74	novel*	b0021	IS1 protein InsB	b0021	IS1 protein InsB
region_1	R	1091390	1091413	23	novel*	b1024	partially deacetylated poly-beta-1,6-N-acetyl-D-glucosamine outer membrane porin	b1024	partially deacetylated poly-beta-1,6-N-acetyl-D-glucosamine outer membrane porin
region_2	F	1105510	1105537	27	novel*	b1044	uncharacterized protein YmdA	b1044	uncharacterized protein YmdA
region_2	F	258193	258280	87	novel*	b4710	IS1 transposase B	b4710	IS1 transposase B
region_3	F	1652252	1652263	11	novel	b1579	Qin prophage; putative defective integrase	b1579	Qin prophage; putative defective integrase
region_3	F	279519	279679	160	novel*	b0264	IS1 protein InsB	b0264	IS1 protein InsB
region_4	F	290990	291150	160	novel*	b0274	IS1 protein InsB	b0274	IS1 protein InsB
region_4	R	2189552	2189560	-8	novel	b2109	putative fimbrial usher protein YehB	b2109	putative fimbrial usher protein YehB
region_5	R	1050074	1050100	26	novel?	b4516	IS1 protein InsA	b4516	IS1 protein InsA
region_5	R	3191402	3191420	18	novel*	b3048	putative fimbrial protein YqiI	b3048	putative fimbrial protein YqiI
region_6	F	1978778	1978875	97	novel*	b1893	IS1 protein InsB	b1893	IS1 protein InsB
region_6	R	4342838	4342846	-8	novel	b4119	alpha-galactosidase	b4119	alpha-galactosidase
region_7	R	3583825	3583945	120	novel*	b3445	IS1 protein InsB	b3445	IS1 protein InsB

ID057

Region	Orientation	X-coordinates	Y-coordinates	Gap	CallType	LeftGene	LeftGeneDescription	RightGene	RightGeneDescription
region_1	R	-1	4518471	4518472	novel	b4403	putative rRNA methyltransferase	b4294	KpLE2 phage-like element; IS1 repressor protein InsA

ID066II

Region	Orientation	X-coordinates	Y-coordinates	Gap	CallType	LeftGene	LeftGeneDescription	RightGene	RightGeneDescription
region_1	F	3414054	3414067	-13	novel	b3265	multidrug efflux pump membrane fusion lipoprotein AcrE	b3265	multidrug efflux pump membrane fusion lipoprotein AcrE
region_1	R	-1	1950820	1950821	novel	b4403	putative rRNA methyltransferase	b1867	putative hydrolase

ID067

Region	Orientation	X-coordinates	Y-coordinates	Gap	CallType	LeftGene	LeftGeneDescription	RightGene	RightGeneDescription
region_1	F	1105536	1105545	9	novel	b1044	uncharacterized protein YmdA	b1044	uncharacterized protein YmdA
region_2	F	1652256	1652263	-7	novel	b1579	Qin prophage; putative defective integrase	b1579	Qin prophage; putative defective integrase
region_3	R	2189552	2189561	-9	novel	b2109	putative fimbrial usher protein YehB	b2109	putative fimbrial usher protein YehB
region_4	R	3191420	3191429	-9	novel	b3048	putative fimbrial protein YqiI	b3048	putative fimbrial protein YqiI

ID068

Region	Orientation	X-coordinates	Y-coordinates	Gap	CallType	LeftGene	LeftGeneDescription	RightGene	RightGeneDescription
region_1	R	315662	316025	363	novel*	b0299	IS3 element protein InsF	b0299	IS3 element protein InsF
region_2	F	392147	392555	408	novel*	b0372	IS3 element protein InsF	b0372	IS3 element protein InsF
region_3	R	567199	567598	399	novel*	b0541	DLP12 prophage; IS3 element protein InsF	b0541	DLP12 prophage; IS3 element protein InsF
region_4	F	1094667	1095071	404	novel*	b1026	IS3 element protein InsF	b1026	IS3 element protein InsF
region_5	R	2170601	2171003	402	novel*	b2089	IS3 element protein InsF	b2089	IS3 element protein InsF

ID073I

Region	Orientation	X-coordinates	Y-coordinates	Gap	CallType	LeftGene	LeftGeneDescription	RightGene	RightGeneDescription
region_1	FALSE	1427941	1428485	544	novel*	b4570	Rac prophage; protein LomR_1	b4570	Rac prophage; protein LomR_1

ID081I

Region	Orientation	X-coordinates	Y-coordinates	Gap	CallType	LeftGene	LeftGeneDescription	RightGene	RightGeneDescription
region_1	R	1427986	1428376	390	novel*	b4570	Rac prophage; protein LomR_1	b4570	Rac prophage; protein LomR_1

ID088

Region	Orientation	X-coordinates	Y-coordinates	Gap	CallType	LeftGene	LeftGeneDescription	RightGene	RightGeneDescription
region_1	R	1474974	1474977	-3	novel	b1406	pyridoxine 4-dehydrogenase	b1406	pyridoxine 4-dehydrogenase
region_2	F	3414053	3414067	-14	novel	b3265	multidrug efflux pump membrane fusion lipoprotein AcrE	b3265	multidrug efflux pump membrane fusion lipoprotein AcrE

ID092

Region	Orientation	X-coordinates	Y-coordinates	Gap	CallType	LeftGene	LeftGeneDescription	RightGene	RightGeneDescription
region_1	R	-1	2422896	2422897	novel	b4403	putative rRNA methyltransferase	b2305	recombination-promoting nuclease RpnB
region_2	R	-1	4537744	4537745	novel	b4403	putative rRNA methyltransferase	b4310	N-acetylneuraminate mutarotase

ID099

Region	Orientation	X-coordinates	Y-coordinates	Gap	CallType	LeftGene	LeftGeneDescription	RightGene	RightGeneDescription
region_1	R	-1	2208346	2208347	novel	b4403	putative rRNA methyltransferase	b2121	VWA domain-containing protein YehP

ID101

Region	Orientation	X-coordinates	Y-coordinates	Gap	CallType	LeftGene	LeftGeneDescription	RightGene	RightGeneDescription
region_1	R	-1	2208311	2208312	novel	b4403	putative rRNA methyltransferase	b2121	VWA domain-containing protein YehP

ID107II

Region	Orientation	X-coordinates	Y-coordinates	Gap	CallType	LeftGene	LeftGeneDescription	RightGene	RightGeneDescription
region_1	R	-1	4537611	4537612	novel	b4403	putative rRNA methyltransferase	b4310	N-acetylneuraminate mutarotase

ID124

Region	Orientation	X-coordinates	Y-coordinates	Gap	CallType	LeftGene	LeftGeneDescription	RightGene	RightGeneDescription
region_1	R	1428004	1428372	368	novel*	b4570	Rac prophage; protein LomR_1	b4570	Rac prophage; protein LomR_1

ID128

Region	Orientation	X-coordinates	Y-coordinates	Gap	CallType	LeftGene	LeftGeneDescription	RightGene	RightGeneDescription
region_1	R	-1	362430	362431	novel	b4403	putative rRNA methyltransferase	b0343	lactose permease
region_2	R	-1	4079649	4079650	novel	b4403	putative rRNA methyltransferase	b3890	protein YiiF

ID130

Region	Orientation	X-coordinates	Y-coordinates	Gap	CallType	LeftGene	LeftGeneDescription	RightGene	RightGeneDescription
region_1	F	381605	382349	744	novel*	b0360	IS2 element protein InsA	b0361	IS2 element protein
region_2	R	2996639	2997441	802	novel*	b2860	IS2 insertion element protein InsB	b2861	IS2 insertion element repressor InsA
region_3	F	3186364	3187082	718	novel*	b3044	IS2 insertion element repressor InsA	b3045	IS2 insertion element protein InsB

ID134

Region	Orientation	X-coordinates	Y-coordinates	Gap	CallType	LeftGene	LeftGeneDescription	RightGene	RightGeneDescription
region_1	R	-1	381345	381346	novel	b4403	putative rRNA methyltransferase	b4579	putative acyltransferase, N-terminal fragment

ID136

Region	Orientation	X-coordinates	Y-coordinates	Gap	CallType	LeftGene	LeftGeneDescription	RightGene	RightGeneDescription
region_1	R	4518572	4518818	246	novel*	b4294	KpLE2 phage-like element; IS1 repressor protein InsA	b4295	KpLE2 phage-like element; putative DNA-binding transcriptional regulator YjhU

ID164

Region	Orientation	X-coordinates	Y-coordinates	Gap	CallType	LeftGene	LeftGeneDescription	RightGene	RightGeneDescription
region_1	R	998706	998715	-9	novel	b0939	putative fimbrial chaperone ElfD	b0939	putative fimbrial chaperone ElfD
region_2	F	1479329	1479339	-10	novel	b1410	hydrolase/methyltransferase domain-containing protein YnbC	b1410	hydrolase/methyltransferase domain-containing protein YnbC
region_3	F	2187361	2187516	155	novel*	b2107	periplasmic protein involved in nickel/cobalt export	b2108	putative fimbrial adhesin YehA
region_4	F	2899337	2899346	-9	novel	b4463	putative FAD-containing dehydrogenase	b4463	putative FAD-containing dehydrogenase
region_5	F	3414053	3414067	-14	novel	b3265	multidrug efflux pump membrane fusion lipoprotein AcrE	b3265	multidrug efflux pump membrane fusion lipoprotein AcrE
region_6	R	3668436	3668445	-9	novel	b3518	cytochrome c peroxidase	b3518	cytochrome c peroxidase

ID177

Region	Orientation	X-coordinates	Y-coordinates	Gap	CallType	LeftGene	LeftGeneDescription	RightGene	RightGeneDescription
region_1	R	274206	274793	587	novel*	b0259	CP4-6 prophage; IS5 transposase and trans-activator	b0259	CP4-6 prophage; IS5 transposase and trans-activator
region_2	R	688108	688689	581	novel*	b0656	IS5 transposase and trans-activator	b0656	IS5 transposase and trans-activator
region_3	R	2066585	2066997	412	novel*	b1994	CP4-44 prophage; IS5 transposase and trans-activator	b1994	CP4-44 prophage; IS5 transposase and trans-activator
region_4	R	2289170	2289752	582	novel*	b2192	IS5 transposase and trans-activator	b2192	IS5 transposase and trans-activator
region_5	F	3130501	3131089	588	novel*	b2982	IS5 transposase and trans-activator	b2982	IS5 transposase and trans-activator
region_6	R	3365800	3366368	568	novel*	b4569	putative uncharacterized protein YhcE	b4569	putative uncharacterized protein YhcE

ID182

Region	Orientation	X-coordinates	Y-coordinates	Gap	CallType	LeftGene	LeftGeneDescription	RightGene	RightGeneDescription
region_1	R	-1	1871913	1871914	novel	b4403	putative rRNA methyltransferase	b1786	putative diguanylate cyclase DgcJ
region_1	R	737424	738254	830	novel*	b0705	putative transposase YbfL	b0706	H repeat-associated putative transposase YbfD
region_2	R	1334887	1334890	-3	novel	b1275	DNA-binding transcriptional dual regulator CysB	b4522	uncharacterized protein YmiA
region_3	F	3000372	3000382	-10	novel	b2866	putative xanthine dehydrogenase molybdenum-binding subunit XdhA	b2866	putative xanthine dehydrogenase molybdenum-binding subunit XdhA
region_4	R	3419943	3419952	-9	novel	b3268	putative ABC transporter periplasmic binding protein YhdW	b3268	putative ABC transporter periplasmic binding protein YhdW
region_5	F	3624672	3624682	-10	novel	b3484	putative transposase	b3484	putative transposase
region_6	R	3652115	3652124	9	novel?	b3504	putative uncharacterized protein YhiS	b3504	putative uncharacterized protein YhiS
region_7	F	3744038	3744043	-5	novel	b3576	DUF386 domain-containing protein YiaL	b3576	DUF386 domain-containing protein YiaL

ID186

Region	Orientation	X-coordinates	Y-coordinates	Gap	CallType	LeftGene	LeftGeneDescription	RightGene	RightGeneDescription
region_1	R	-1	2208341	2208342	novel	b4403	putative rRNA methyltransferase	b2121	VWA domain-containing protein YehP

ID187

Region	Orientation	X-coordinates	Y-coordinates	Gap	CallType	LeftGene	LeftGeneDescription	RightGene	RightGeneDescription
region_1	F	1427985	1428355	370	novel*	b4570	Rac prophage; protein LomR_1	b4570	Rac prophage; protein LomR_1
region_1	R	1217589	1217598	-9	novel	b1168	putative c-di-GMP phosphodiesterase PdeG	b1168	putative c-di-GMP phosphodiesterase PdeG
region_2	F	1747255	1747264	-9	novel	b1668	FAD/NAD(P) binding domain-containing protein YdhS	b1668	FAD/NAD(P) binding domain-containing protein YdhS
region_3	R	2042730	2042740	-10	novel	b1974	putative cytochrome	b1974	putative cytochrome
region_4	R	4518692	4518693	1	novel?	b4294	KpLE2 phage-like element; IS1 repressor protein InsA	b4294	KpLE2 phage-like element; IS1 repressor protein InsA

ID197

Region	Orientation	X-coordinates	Y-coordinates	Gap	CallType	LeftGene	LeftGeneDescription	RightGene	RightGeneDescription
region_1	FALSE	3414053	3414067	-14	novel	b3265	multidrug efflux pump membrane fusion lipoprotein AcrE	b3265	multidrug efflux pump membrane fusion lipoprotein AcrE

ID214

Region	Orientation	X-coordinates	Y-coordinates	Gap	CallType	LeftGene	LeftGeneDescription	RightGene	RightGeneDescription
region_1	F	1581836	1581844	-8	novel	b1498	putative sulfatase	b1498	putative sulfatase
region_2	F	3414054	3414065	-11	novel	b3265	multidrug efflux pump membrane fusion lipoprotein AcrE	b3265	multidrug efflux pump membrane fusion lipoprotein AcrE
region_3	R	3668436	3668445	-9	novel	b3518	cytochrome c peroxidase	b3518	cytochrome c peroxidase

ID229

Region	Orientation	X-coordinates	Y-coordinates	Gap	CallType	LeftGene	LeftGeneDescription	RightGene	RightGeneDescription
region_1	R	-1	2208351	2208352	novel	b4403	putative rRNA methyltransferase	b2121	VWA domain-containing protein YehP

ID231

Region	Orientation	X-coordinates	Y-coordinates	Gap	CallType	LeftGene	LeftGeneDescription	RightGene	RightGeneDescription
region_1	F	258291	258294	3	novel	b4710	IS1 transposase B	b4710	IS1 transposase B
region_2	F	1978886	1978889	3	novel	b1893	IS1 protein InsB	b1893	IS1 protein InsB
region_3	R	3583728	3583811	83	novel*	b3445	IS1 protein InsB	b3445	IS1 protein InsB

ID237

Region	Orientation	X-coordinates	Y-coordinates	Gap	CallType	LeftGene	LeftGeneDescription	RightGene	RightGeneDescription
region_1	R	-1	2208341	2208342	novel	b4403	putative rRNA methyltransferase	b2121	VWA domain-containing protein YehP

ORTHO055E

Region	Orientation	X-coordinates	Y-coordinates	Gap	CallType	LeftGene	LeftGeneDescription	RightGene	RightGeneDescription
region_1	R	315645	316025	380	novel?	b0299	IS3 element protein InsF	b0299	IS3 element protein InsF
region_2	F	392086	392555	469	novel?	b0372	IS3 element protein InsF	b0372	IS3 element protein InsF
region_3	R	567194	567589	395	novel?	b0541	DLP12 prophage; IS3 element protein InsF	b0541	DLP12 prophage; IS3 element protein InsF
region_4	F	1094622	1095079	457	novel*	b1026	IS3 element protein InsF	b1026	IS3 element protein InsF
region_5	F	2171050	2171086	36	novel?	b2089	IS3 element protein InsF	b2089	IS3 element protein InsF
region_6	F	3301809	3302069	260	novel*	b3158	putative peptidase YhbU	b3158	putative peptidase YhbU

ORTHO08HW

Region	Orientation	X-coordinates	Y-coordinates	Gap	CallType	LeftGene	LeftGeneDescription	RightGene	RightGeneDescription
region_1	R	-1	3109802	3109803	novel	b4403	putative rRNA methyltransferase	b2966	DUF554 domain-containing protein YqgA
region_1	R	-1	4518471	4518472	novel	b4403	putative rRNA methyltransferase	b4294	KpLE2 phage-like element; IS1 repressor protein InsA

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Citations and Bibliography

If you have used rMAP, please cite:

Sserwadda, I., & Mboowa, G. (2021). rMAP: the Rapid Microbial Analysis Pipeline for ESKAPE bacterial group whole-genome sequence data. Microbial genomics, 7(6), 10.1099/mgen.0.000583. https://doi.org/10.1099/mgen.0.000583

The philosophy of rMAP was built on the foundation of already pre-existing tools. As a token of gratitude to the authors of those numerous tools, please also cite:

• ABRicate, T. Seemann
• AmrfinderPlus, Feldgarden M. et al., 2019
• Any2fasta, T. Seemann
• Assembly-stats, Sanger Pathogens
• Biopython.convert, biopython.org
• Bwa, Li H. et al., 2009
• Bmge, Criscuolo et al., 2010
• Cairosvg, cairosvg.org
• Fasttree, M.N. Price et al., 2009
• Fastqc, Andrews S., 2010
• Freebayes, Garrison E. et al., 2012
• ISmapper, [Hawkey J. et al., 2015
• Iqtree, Nguyen L. et al., 2015
• Kleborate, Holt KE, 2020
• Mafft, Katoh K. et L., 2013
• Megahit, Li D. et al., 2015
• Mlst, T. Seemann
• Multiqc, Ewels P., 2016
• Nextflow, Tommaso et al., 2017
• Parallel, O. Tange, 2011
• Prodigal, Hyatt D. et al., 2010
• Prokka, T. Seemann, 2014
• Quast, A. Gurevich et al., 2013
• R-base, R Development Core Team, 2008
  • ggplot2, H. Wickham, 2009
  • ggtree, G. Yu et al., 2016
  • knitr, Y. Xie, 2015
  • plotly, C. Sievert et al., 2017
  • RColorBrewer, E. Neuwirth and R.C. Brewer, 2014
  • reshape2, H. Wickham, 2007
  • rmarkdown, J.J. Allaire, 2015
  • treeio, L-G. Wang et al., 2019
• Roary, A.J. Page et al., 2015
• Samclip, T. Seemann
• Samtools, Li H. et al., 2009
• Shovill, T. Seemann, 2020
• Snippy, T. Seemann
• SnpEff, Cingolani P. et al., 2012
• Tormes, Quijada NM. et al., 2019
• Trimmomatic, A.M. Bolger et al., 2014
• Unicycler, Wick RR. et al., 2017
• Vt, VT

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